So, you think you have it bad that your Atom Hackintosh will forever stay on 10.6.1?
Guess what, my PowerPC *genuine* Mac will forever stay on 10.5.8.
Apple is often not supportive even of older hardware they sold few years ago.
As mentioned, Mac OS X 10.6.0 doesn't support the PowerPC CPUs while the 10.5.x did. I have a fairly strong (even by today's standards), last generation G5 PowerPC Mac that I bought in December 2005 (one month before they confirmed the Intel switchover rumors) that is now doomed to never run Snow Leopard. I could now go around and holler "APPLE BASTARDS BLOCKED PowerPC IN 10.6.0", right?
Or I could be annoyed by the fact that even when Leopard came out, PPC experience was already "downscaled" compared to Intel Leopard - i.e. no Java 6, no support for certain HD video codecs, etc.
Heck, not even Macs with 32-bit Intel CPUs could have Java 6 under Leopard. Curiously, they do in Snow Leopard, but I digress.
Recent news was that on some older (2006) Intel Mac models (some of them already 64-bit), you won't be able to install Windows 7 via BootCamp. (This one I don't care much about, but some people certainly will.)
As you can see, even their own hardware gets left in the dust. I'm not ruling out deliberate malice on their part, but I'd rather assume they recompiled the kernel and libraries with compiler options that benefit their current CPU lineup the most, and it turned out to be incompatible with Atom, and they shrugged and said, "so what? We aren't supporting any hardware with Atom CPU anyway". Even if they did it deliberately, they can just claim that they did it as an effort to optimize performance for their current hardware.
At the end of the day, there's many more Hackintoshes out there than just Atom-CPU based ones, why would they go after specifically after the Atom ones? Those aren't even competition to Apple's hardware business - Apple doesn't have a netbook offering, and they don't consider MacBook Air to be one. People buying a netbook aren't a market Apple targets.
So, I think it's much more plausible that end of (accidentally working until now) Atom support is being a collateral effect of them doing some improvements. However, if it's not deeply baked in, then I'm sure the Hackintosh crowd will manage to get around it.
In any case, they have much better chances of it than me seeing Snow Leopard on my PowerPC Mac.