It has nothing to do with the app store from a technical perspective. It removes one of the reasons people would want to take the time to hack it.
The geeky in nature are still going to want to 'control' their devices. And since they're not making money off this (well some of the developers are that distribute apps), I doubt that has a strong influence at all in the delay of a 2gen method. Especially since the app store was out during the 1st gen, and we've seen them successfully break each firmware release within days.