For that matter, is 64-bit any better than 32-bit?
Yes, mining on linux will give you a -little- fast result, result of the less overhead from linux. Don't think 86/64 makes a difference.
Care to quantify that? Does it reduce output by a percentage or just a set amount? I'm more familiar with windows (making a miner run on bootup, etc) so if the difference is negligible that would probably be the route I choose.
If Windows is what you know, I would definitely stick with Windows. Linux is my OS of choice but that's just because I am a Linux user/admin so it's where I am comfortable. Linux may have lower overhead but Windows does have advantages. Particularly, controlling the voltage and GPU/memory clocks is more flexible under Windows. You have things like afterburner which us Linux users currently lack. There are Linux solutions to be sure, they just are not as refined as their windows counterparts.
May I ask what MB/case into which you intend to cram a tripple 6990 rig? That's a lot of heat.