Yeah, once she's a kid. Babies are a pain in the ass, logistically speaking. It actually makes sense that he would wait to spring this one on Harry until the kid was older. There is no way Harry would have let anything else take priority over a kid, and including an infant or toddler in the story is adding all sorts of diversions and distractions to Harry's life, giving him a different perspective and priorities, that might have made some of the other choices and risks he took counter-indicated. People are always snarking about how convenient the new baby on a TV show is, crying and making a fuss when the writers want to inconvenience the characters, and conveniently behaved with the world's most amenable sitter while the parents are doing more interesting things. Dropping dramatically ironic hints of her existence that Harry would miss (like the Lasciel foreshadowings in this book) would only make him seem stupid once it was obvious to the readers that Susan was pregnant or had a kid. Dealing with a single character's knowledge and perceptions means you have no other way of letting the readers know, like some sort of coda to Blood Rites, where after Harry is reveling in his newfound family connection, we cut to Susan giving birth in a Fellowship safe house, and saying "Her name is Maggie. What's that? No, the father is not in the picture."

It's a spirit of intellect. I'm pretty sure gender isn't really relevant to the parasite kid. What makes sense is that he'd have pushed it's gender in the direction of all the people with whom he has a loving relationship, if he had any subconscious influence on that issue. Or maybe it picked a semblance of femininity because of Harry's putting-women-on-pedestal issues. I think giving Harry two very different types of daughters is like Robert Jordan giving Rand three different love interests: he can show more than one kind of relationship. He can have the guiding-the-power mentor thing with the mindbaby, while protecting Maggie's innocence.

Also, as far as the gender thing goes, there is a reason why they are both girls, and it is the same reason why Arnold Schwarzenegger only has daughters in his movies - daughters are weaknesses who must be protected, while sons represent continuity and are an extension of the father. An action hero character only fathers a son right before he's going to die. Or else his son dies to send him on a suicidal vengeance run. It's probably not even a conscious thing on the authors' part - it's just a whole bunch of unwritten rules and cultural values that shape our perspective of generic children. Daughters are to be cared for and protected, NO MATTER WHAT. So even if the mindbaby becomes a giant pain in the ass, no one will seriously question his commitment to trying to protect "her". That's what you do with daughters (which is also why in every movie about a male character dealing with unexpected fatherhood, or adjusting to the travails of being a parent, he has a daughter. Seth Rogen had a girl in "Knocked Up" because that movie was about him maturing into someone who can be responsible for providing for and caring for a kid. Adam Sandler was left with a boy in "Big Daddy" because his character was already financially secure, and the movie was about him turning the kid into a playmate - an extension or continuation of himself, in other words. The only role kids can really have in Harry's story are as things to take care of, protect or rescue, so you need girls for those roles. Hence Maggie & the mindbaby both being the same gender.

Personally, I find it more "too convenient" and eye-roll inducing when the author gives his hero a twin boy & girl route.

IDK, there was a lot of that stuff in there about Thomas' unexplained interest in Harry, and motivations for helping him. And Ebenezar's description of his relationship with Maggie Sr practically screamed 'father-daughter.' His interest in Harry, to the extent of involving himself in politics and taking a Senior Council seat against his prior disinclination, solely to protect him, always came across as more paternal than pedagogic.

I thought there were.
Recall too, Butcher was not that good or subtle in the early books. He didn't really start to get the tone I think of as typical of the series until around book 5 or so. Before that, leaving hints like you describe might have come out sloppy or awkward. Blood Rites, though, had a very definitive theme of family issues and dysfunction, to the point that it seems to be all but screaming "Hey, look. Harry & Ebeneezer are doing it too, and he's decribing doing it with Margaret!" His specific description of how he pushed her too hard, leading her to rebel and then hook up with Lord Raith, before settling down with Malcolm Dresden went right along with Thomas' stories about his upbringing and the wierd manifestations of affection between him and Lara, and his attempt to protect his sister from their family legacy. There was the happy ending of the porn stars all quitting to start families, from Arturo & his producer/wife, to Jake taking up the parenthood mantle to Inari & Bobby making plans together. There was Murphy, discussion of her filling her father's shoes, the revelation of her mother's knowledge of what she does, and how that affects their relationship and the ways they lie to one another out of love, and of course, making a thing about her ex-husband marrying her sister. And it's just supposed to have been a coincidence that this is the book where Harry has a falling out with his mentor and secret grandfather, over issues that tie in with their relationships to Harry's mother? Nah. It was definitely on Butcher's mind at the time.
From what Nicodemus said about trust, that was just too important to trust to someone being forced for any reason. From a dead person's perspective, threatening to kill a loved one is only a threat to hasten their reunion. What father would not prefer his child to join him in the next life, rather than live a hair longer under the dubious mercies of Nicodemus? The point was that he had long since burned all his credibility, and there was no one who could take his promise, or who would be willing to trust that he would live up to his end and actively remove a threat to their family members, because that is totally not the sort of thing Nicodemus does. Once he got what he wanted, killing the hostage is absolutely a typical Nicodemus move.

Another issue to remember is the point of the scam was to get him to kill his daughter. For all we know Mab & her partners fed him false information that precluded any other course of action.

You forgetting about the mind-baby?

Mab established when she showed up that she's been blocking people from coming, and Ebenezer visited his grandson exactly as many times as Harry visited his own daughter. Why would he come when he has never come to Chicago except on wizard business in the rest of the series? It's also stated more than once in the two previous books that the White Council has their hands full in the turmoil following the power vaccuum the Red Court left, there were some internal breakdowns as a result of the Red peace talks, AND he's running the Grey Council as well. At the end of Turn Coat, Harry & Ebenezer were operating on the assumption that the new Senior Council member was a Black Council operative or dupe, so it makes sense that he would stick near the centers of power and Ebenezer would stick near to keep an eye on him (probably why he insisted on being on the stage with Cristos and Arianna, when the rest of the Seniors were just illusory).
And Michael gave the reason for that in this book - the island is an oppressive presence that deters other people from going back. Harry notes in spite of that, Thomas and Murphy did actually visit him there a couple of times, so it's actually completely the opposite implication.