Moiraine is one of my favorite characters, but the AS in general just aren't very smart. The Prophecies say that the DR will be "of the ancient blood but raised by the old blood", which would narrow the search for him down to areas that were predominantly old blood: the two rivers, perhaps the borderlands, essentially any country that had not intermixed its blood with others'. This would automatically rule out Altara, Murandy, and large swathes of other countries. The only reason for the AS not to have seen that off the bat is because they are pigheaded. So, I get that Moiraine didn't look into the two rivers until the very last, but given the dumb white tower background she came from, that's mostly an indication of how foolish the Tower - and people brainwashed into its way of thinking - really are. Not because the two rivers was somehow an unlikely suspect.

If the search really included the whole world, there's no reason to waste resources on specialized hounds until it's narrowed down (by a lot). You could just use the pre-existing resources - regular DFs, BA, BA spies, etc - until the search is narrowed down. Only once the search is narrowed down to a specific area would it be profitable to start using specialty hounds to seek out the exact person. If hounds had been sent to every region in Randland, then presumably there'd be one for each country/area, or near enough; one for Ghealdan, one for Andor, one for Murandy, etc. But instead, we see Fain tasked with multiple areas, a wide swathe including all of Ghealdan, Western Andor (an area including the two rivers as well as Baerlon), norther Murandy. To me, this indicates that the Shadow had narrowed the DR's location down to that single area and sent a single "hound" (Fain) to search for him. Were Ghealdan and Murandy dumb areas to include if the Shadow had read the KC? Yes. Is the Shadow always necessarily very smart? No. I don't remember for sure, but I assume Fain was made/sent by Ishamael; who was half mad at that point. If the Shadow had still been looking in a wide area, and that wider area only happened to include Fain's search region, then I'd think Fain would have been given a less sloppily-bordered area to look in, and I'd think Ishy, the DO, or Fain would have mentioned it by now.

So personally, I don't think there were any other hounds besides Fain. The shadow could have just used traditional resources to narrow the search area down, and once it had a specific small area to search in, Ishy or the DO grabbed Fain and imbued him with special powers to take the search the next step. But, I could be wrong. If I am wrong, and there were multiple hounds of which Fain was only one of many, then I believe that any other hounds are probably long dead by now.