I'm not a realtor..but I don't think it will affect the value either way, as long as whatever you do looks like it belongs and is quality construction. If your current attached garage isn't finished inside, just studs, that's great, because you can put soundproofing insulation in! I think budget wise, it would probably be cheaper to build another garage. I would never cover up windows if I could avoid it,( and I wouldn't buy a dark house either).
I'm all for the storm shelter even if you do nothing else!! Tornados are mean and scarey things. Even straight wind can be very dangerous. Peace of mind is what your after here (and maybe enough room for the drum set?? :lol: )
I see now you have a HOA? Will they even allow you to build a detached garage? They will throw a wrench in the works for sure! Maybe an app't with an architect would help, they might be able to come up with a better plan than covering up windows. Good luck!