It is entirely possible over a period of time they will introduce upgrade App Store pricing for higher priced items, but I did not see anything yesterday that indicated there was a version available other than the full one. However, as noted, when you're paying $79 it doesn't really matter. You're getting the full version for less than half the prior cost.
I don't know if Aperture 2 and 3 can coexist (most likely they cannot run simultaneously, based on past experience with these kinds of questions) but the current version has many performance enhancements and bug fixes relative to the original shipping version so if that's what you're worried about, I think you're safe to switch.
