Details easily figured out. In answer to your specific questions: Sometimes; no; no; it immediately switches to your side and you have to make it run to safety; no; yes but its at almost no CR so you can't really fight with it; crew is transferred, some changes to crew mechanic are needed.
Yes this could also be done by having one, very simple dialog after battle where you can decide to capture as many ships as you want with 1-2 clicks each (no options about shuttles which are a waste of time in a game of this scale)
The reason for having it in combat is that it creates actual different objectives in combat. It's another thing you can order your AI ships to do. As I said, combat is uninteresting and repetitive since you're always doing the same thing.
That's great! I can see that working woonderfully.
Now imagine how much work is going to be involved in creating and debugging this behaviour.
Why would you do all that work when you already have something that works perfectly fine in place already?
If shuttles are a waste of time then how do you even start a game?
Sure they're a pain when you have dozens of them, but there's a thing you see that makes all that clutter go away. That thing is called: Frieghters.
If you're getting annoyed by shuttle clutter it's your own fault for dragging them around everywhere when you just don't need to. You don't need any more than 2 or 3 in a fleet for boarding anyway.
The thing about having boarding in combat is that it is very easy to turn that into some kind of "twitch" mechanic where you are forcing the player to do <thing> in a certain way at a certain time, and that is something I feel needs to be avoided at all costs.
If it's going to be a simple as get close to enemy, launch shuttles, watch progress bar until victory (or not) then that's cool.
If it's going to be a mini game of some kind, or require super reflexes and timing then it would be an utterly horrible experience.