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Hi Chris,
Canons are traditionally considered more astro friendly probably since the 20da was released. More people seem to use canons which is why you see more modified canons. I wouldn't worry too much about this unless you were planning on a professional cooling mod like done at central ds. also astro software was usually aimed at canons, now you have backyard Nikon (in addition to eos) to control your camera.
Yes APS-c chips are more friendly because they are generally less affected by the edge of the imaging circle (where things go pear shaped quickly). You can always just crop the final images of your Nikon. I probably wouldn't worry about getting a canon unless you were really pedantic about this. the other benefit of an aps c is if you are taking planetary movies, the planet will appear much smaller on the full frame. as dslr's are often used as all rounders to begin with that makes aps-c a more cost effective option.
as for $300 vs $thousands you would be surprised what image stacking astro processing can do. the more expensive ones usually do better on a single exposure (good for nightscape) but that is fairly quickly negated on deep sky stacked targets.
Russ
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