1) Does MoM run in a window? At what resolution?
2) Does the GOG version of MoM use DOSBox?

It's MS-DOS game so obviously it uses DOSBox. There was never a Windows release. As all dosbox games, it can be run in window. I believe resolution is 640x480 and I think you can get higher resolution using scalers but I don't have much experience with dosbox configuration so you'll need to ask someone else about it..

Yep, there's a "scalar" entry in the .conf file. I think it contains a list of scalars in the comments, too, or someone who's got them memorized can tell you what they are. Or Google. :)
As for getting it to run in Windows, I'm only a hobbyist programmer, but, AFAIK, that would require re-writing a lot of the game - The entire GUI and sound system, at a bare minimum. Probably some other things I don't know about. Or, they can save some work and use DosBox.
I'm pretty sure they re-compiled Interstate '76 from code, because I remember it not working so well in XP before. In the case of I'76, it would be easier, because it's already a Windows game - Most of what they'd be doing is probably "find and replace, done by humans".

Just to clarify, the game runs in 320x200 resolution. Of course, as Petrell says, you can scale the resolution of the title to suit your needs with DOSBox. There are two threads detailing how to do this.