Why yes, I do have a huge rambling discussion on the design of those shuttles.

Part of which is that, once more, those aren't windows, at least not normally. They're a modular section that normally has an extra layer of shielding and reinforcement for the cameras and a bunch of other monitoring equipment. But it can be optionally removed (the process takes about 6-7 man-hours and some special tools) and replaced with reinforced transparents if one thinks they'll be seeing a lot of combat where the cameras are likely to get knocked out by the electronic end of the combat process.

And that's one small section, like I said it's a long rambling thing.