It appears that Atom support has resurfaced in the latest developer build (10C535), so users running OS X on Atom netbooks are safe, for now. Although, anything can happen between now and the final build. [Stell via 9to5Mac via Crunchgear]
I don't believe Apple would resort to crippling support for the Atom for a couple of possible reasons:
-They have a close relationship with Intel. While Apple is notorious for playing roughly with others, I don't believe that they would want to be at odds with Intel over something like the Atom, or even general artificial discrimination of their OS towards a number of their products.
-They might actually use an improved version of the Atom one day. Though most speculate that Apple will never bother, it sounds like a pretty unreasonable bridge to burn.