Very unlikely. If the MKV video stream is in h.264 and you use Perian + QuickTime Player, it might use hardware acceleration where available, but I can't be sure on that at all.
Also note that the H.264 hardware acceleration is only currently available on the Nvidia 9400M chipset, not on any of the others.
Main reason i got Snow Leopard was for the GPU acceleration for 1080p video playback, but quick time X doesnt support mkv fileformat, so is there any way to play mkv with GPU acceleration?
Actually, any OpenCL-capable GPU (such as the 9600GT found in the high end MBPs) will support hardware decoding. I've tested this on both my 9400M and 9600GT (MBP 2.66C2D, 4GB RAM, 512MB VRAM 9600GT, 256MB shared VRAM 9400M).
EDIT: yes, h.264 and x264 are the same codec.
MKV isn't a format, it's a container. 90% of the HD .mkv's that you see floating around are going to be encoded in MPEG4, so rename the file from .mkv to .mp4 and quicktime should play it without a problem.
Main reason i got Snow Leopard was for the GPU acceleration for 1080p video playback, but quick time X doesnt support mkv fileformat, so is there any way to play mkv with GPU acceleration?