I was also a little disappointed to find that only 50% of my books were indexed. But I've since developed more perspective :) An EYB person told me that about 60% of the books that are actually on members' shelves (as opposed to being in the database but not on any shelves) are indexed, and as saladdays said, more are being indexed all the time. I have quite a lot of older books that are on only on a handful of shelves (in a couple of instances only on mine!) and it's understandable that EYB aren't giving priority to those.
I've indexed a couple of my own books, giving priority to ones that a) are on few shelves, b) aren't too long, and c) I haven't used for a long time -- since part of the point of EYB for me is to rediscover neglected cookbooks. It's time-consuming, so I don't suppose I'll do this for many books, but I'm happy to do it from time to time since I do benefit from it.
I suggest you go through your unindexed books and whenever you find one that's on at least 10 shelves, request an EYB index. It's my understanding that the more members who ask for a book to be indexed, the higher up the queue it goes.