I try and find a balance between the two.
I aim for low ISO. So when doing night shots, at ISO 100, if my shutter is getting too high (say 30 secs), I'll up the ISO to 200 to get it down lower. But thats about the only time I don't shoot at ISO 100.
The long exposure shouldn't matter as you should be doing long exposures on a tripod.
Light noise from long exposures are dependant on the lighting conditions and other factors present at a specific scene and may not happen in a different scene with similar settings.
Noise from high ISO will happen more often. As in I know my camera sucks at ISO 1600, so I don't shoot at that ISO. Some scenes seem to be better than others though.