Aperture does not support alpha channel so the images would not show in Aperture with transparent backgrounds. However the files should not have been damaged in anyway as Aperture does not modify the master.
As for future support. No one can say what Apple will do but given the purpose of Aperture I doubt alpha channels will ever be supported.
So I take it nothing Apple makes supports transparency correctly. iPhoto sorta does but if the image is black on transparent you see a black box (I have about 400 of these) Aperture has no support at all and finder puts a white box around them so my white PNGs (again about 200 of these) can't be viewed in finder when I make the folder backgrouns gray. This is so annoying.
But it is clearly stated (well, in one of the footnotes ) in the tech specs of Aperture, http://www.apple.com/aperture/specs/
see the footnote 2:
Aperture maintains but does not display layer and alpha channel information in PSD files.
Aperture is designed to handle images imported from digital cameras:
Using Aperture, you can import JPEG images from virtually all digital cameras. Shooting RAW? Aperture supports the RAW formats from a wide range of digital SLRs and medium-format cameras and camera backs. You’ll find an extensive list of supported camera models on the RAW support page.