I think it's mostly because it's harder to market two apps than one. From my experience (I'm also developing educational apps for kids), what makes an indie iOS app a success is more and more determined by Apple's decision to feature it, and going up in rankings. With two apps, it'll be twice harder to get in the top 10, and you'll have to choose between one of them to be featured.

And from what I've seen, the paid-IAP users' reviews get lost in the free reviews. You split your high-quality reviews (from people who like it well enough to pay) into two pools, and then poison one of them. Worse yet, since people tend to try free versions first, you're funneling a lot of people into the poisoned review pool.

Our Maths stuff has not been featured (not counting What's Hot, which is algorithmic as far as I can tell), yet it has hit top grossing in the category in a few major stores.

I'm wondering whether Apple will ever offer either: 1] a dedicated education app store, invisible to non-volume purchasers. 2] a mechanism for allowing volume purchases of in-app content.