One important thing everyone here is not taking into account: Aperture is/was designed and built from the ground up by Apple. It was simple for Apple to put Aperture 3 on the Mac App Store, because Apple controls 100% of the Aperture code base.
Logic was bought from a German software developer called Emagic. At the time, the software was still available on the Windows platform. Apple killed that, but continued to develop Logic for Mac on the same foundation. I remember being quite upset about this, as I had access to Logic Platinum in the studio...
Final Cut Pro was based on early Adobe Premiere Pro code. Up until Final Cut Pro 7, the same code base was built upon and it was only with Final Cut Pro X that Apple had rewritten the code from scratch, thus making it possible to put Final Cut Pro X on the Mac App Store -- no licensing (or patent) issues.
What upsets me however, is that Apple at the time bought Color, a twenty-thousand dollar application and essentially killed it with the release of Final Cut Pro X. The asking price for the previously available Final Cut Studio was really minuscule if you do the math. I hope Logic will not suffer a similar rewrite of the code base. I have to say that I'm enjoying Final Cut Pro X so far, but will have to use Adobe Premiere Pro for work. $400 for an advanced video editing system is reasonable. Notice that I said 'advanced', not 'professional'.
The reason I reminded you of these facts is that Apple developed Aperture in the first place and has controlled every aspect of Aperture development since version 1.0. Unless Apple decides a rewrite of the code base is needed, I think it is safe to assume that Aperture will retain its look-and-feel even in version 4, which I personally suspect is coming in early / mid 2012.
Have a nice day.
~Yousif