Now you got me confused, about how you counted that. When I look at your bookshelf, I see 54 of 104 books indexed - over half. Of the books with over 100 members (which we can safely assume are the more popular ones) 40 were indexed and 1 was not. I'd think that was a pretty good score.
Now, what to do with non-indexed books? Indexed books are more useful than non-indexed ones, it's true. Of course you can index the ones you really want indexed yourself. The other ones are catalogued - I do like to have a list of my cookbooks, although I do admit sites like LibraryThing are better if catalogueing is what you're after. You can also still make notes even if a book isn't indexed. But mainly, they are on hold. The main point of having unindexed books in your library is that when they become indexed, they are available to you rightaway and you don't have to keep checking if your books are being indexed.
EYB is a work in progress, but I definitely prefer an incomplete database to no database at all.