I'm not 100% sure I fully understand what the problem is, I guess mainly because I'm not 100% sure what these apps will do, exactly. Will they take the place of websites and compete with them, or are they something that webmaster will release in addition to their sites? If the former, then it could potentially be a slight issue for some people - but I don't imagine it would be a noticeable one. If the latter, then it could be even less of an issue from a domainer's point of view.
If they're competing with websites, I imagine it would take more work for them to be popular than websites. How many of these apps do you think people will want to keep on an over-sized iPod Touch (or whatever competition comes against them)? The fewer of these apps someone wants to keep on their device, the more difficult it will be for these developers to keep them popular enough to be worth running. Not only that, but if someone makes one of these apps as a source for information rather than making a website, how many people are they really going to reach? How many people will own an iPad? That's like making a website to only be compatible with Opera, except worse. Why limit your focus so much? Also, how will people find these apps? Don't you think the developer would need a website?
If developers are creating apps to coexist with their websites, they still need the domain. What's the issue? Their site will be getting less traffic because the app will take some, so the name is worth less? I doubt it. If anything, they may be more ambitious for the name they want since they're spreading to multiple platforms and they'll likely be keeping the same name along the way.
Maybe I'm completely wrong, way off, going the wrong direction, complete 180, inside out and backwards... or something... I don't know. If nothing else, I'm something for the experts to pick apart, an opposition, an antagonist, a rival, an adversary.