I am not an app developer so I have no idea but I'm sure there are a few here on Crackberry. I do however have lots of experience with Paypal and typically they charge 30 cents plus 3.9% for a fee. With that charge plus the 20% Blackberry charges, it wouldn't be worth making an apps for 99 cents.
So app developers, do you know if that has anything to do with it?
I do find it interesting that Blackberry is excluding the 99 cent and 1.99 apps which are widely popular for Apple (I know others have posted this comment before, I just agreeing with them). I think in the future they will realize they are missing out on a huge opportunity.
Developers aren't told much more than the general public, but heres a little run down of how we are paid:
We are given 80% of the commission for each sale, which for a $2.99 app would be ~$2.392.
RIM takes the remaining 20% to cover all transaction fees and keeps whatever they have left.
I think you're right on track with the reasons why RIM is avoiding $0.99 applications, 20% of $0.99 is $0.208. That means RIM would be paying from their pockets to cover the transaction fees.