App Store app is just a different interface to the itunes servers, you can try to copy links in App Store and you'll see the exact same kind of url as for tunes, movies, iOS apps, etc...
In fact I don't understand why they didn't integrate App Store in iTunes. Maybe they realized iTunes is crap, or they didn't want to change the icon once again.
Doesn't make me feel like they have long term strategies lately.. kind of the same with Facetime desktop not being in iChat.
I’m not sure those technical details matter at all.
If you ignore iTunes, Apple doesn’t do kitchen sink apps. Their apps might not have razor sharp focus (you can do a lot of different stuff with iPhoto) but in general they stick to one theme (but everything in iPhoto has something to do with photos). I’m a fan of the hypothesis that the only reason iTunes does so many different things is that it has to run on Windows. Apple might not want to ship a few different apps for Windows, they might want to keep it all together. Apple might already have split iTunes into a few different apps if they only had to run on the Mac.
The App Store doesn’t run on Windows, it doesn’t have the same problem so Apple just reverted to their default non-kitchen-sink approach.
In fact I don't understand why they didn't integrate App Store in iTunes.
The App Store installs itself as the second-highest icon on your Dock, just after the Finder. That's an amazingly prominent placement.
Remember that most people will be getting the Mac App Store unwittingly as part of the Mac OS X 10.6.6 update. If they didn't have a separate Dock icon for it, those people would never find out it exists.