I had my son when I was 19. I didn't give him his dad's last name, he has my maiden name. When I got married two years ago and had my daughter there was definite discussion about changing his name with him. He was just short of nine when Alana was born and he and I had several talks about what he wanted to do. He finally decided he would like to keep his last name, he likes it, it is unique (and it is, I miss it when I fill out forms. It's one of my middle names now), and he's the last male in our family with that name and at the age of nine he was deeply concerned that the name would die off. He's so cute and so worried about things that he shouldn't even know about.
Having a different last name as his sister doesn't affect him, at least it hasn't yet. Some mean kids at school tried to tell him that Alana isn't his real sister because she's his half sister, but those kids adore each other and ultimately he knows that it only matters how they feel about each other.
My parents didn't care if he changed his name or not, so long as he was happy.
I guess the real differences are that he was old enough to choose and it was my name not his dad's. I hope things work out well for your family!