That's a good question. Part of it is not want to have the other person's books cluttering up our home pages! (This is where we REALLY need folder capability.)
That said, is it too late for us to combine accounts as this point?
What do other 2-Kindle homes do?
You don't have to have all of the books on both Kindles. They will, however, all be visible on your Amazon Manage Your Kindle page. I agree with Leslie, contact customer service (call them: 1-866-321-8851). You can, by yourself, de-register one Kindle from it's account, and register it on another, but I imagine you would need customer service intervention see if you can move ebooks already purchased to the other account. Call them first before doing anything. Please let us know how it works out, this will be good info for Leslie's FAQ.
My husband and I both have a Kindle, they are both on my account. I buy all the books, he doesn't know what he's doing.

FYI, you can share books on one account, but not subscriptions.... like newspapers and magazines.