I would think your best bet would be to let your kids get there autographs and then approach them yourself with the book for your niece and nephew and briefly explain that it's for kids in your family who couldn't made the trip. I'd be hesitant to get separate autographs for each of them if they can't share one book. As quite a few other people have mentioned, the characters are only out for a limited amount of time and the more time they spend signing autographs for you niece and nephew, the less time they have to spend with other kids who actually are at WDW.
Personally, I feel like the autographs are special because they remind the child (or adult!) of the experience of meeting the character, though maybe your family feels differently. Still, I would think about whether going through the trouble of getting autographs is the best way to bring a piece of Disney home to your niece and nephew. Is there a souvenier they would really enjoy? Or maybe you could split the difference. Have them each pick out a favorite findable character, buy a shirt or hat or something with that character on it, and have the character autograph that one thing. That way, your niece and nephew each have a special autographed Disney memento, and you aren't holding up every line for the characters you get into.