I'd say that most applications with two distinct words in the name use uppercase, and most apps with single or compound words use lowercase. My guess (remember, it's just a guess) is that the exceptions are about legibility. For example, if the icon for Illustrator said AI instead of Ai, people may wonder what Adobe Aluminum is
BTW, the typeface was designed by Robert Slimbach, one of the greatest, living masters of type design.
Also, I think this entry in Adobe's blog on type, Typblography, is very interesting.
Interesting question! Personally, I think it's just a matter of design and/ore legibility, perhaps being conscious of foreign languages as well. InDesign and On Location also have caps in their second character, along with a few (like Photoshop) which could be lower or upper, it's hard to tell.