So Bond pistol-snipes the whole breaching team without waking the kids?
I'd personally want my family to know to get to safety whether or not I'd given them a heads up. Gunshots are generally a good indicator to get out of bed, lock the door and call the police.
If you've ever hunted, you know the bang doesn't bother much in the moment. I consider noise a non-issue in defensive situations. As for flash, I'll avoid shooting hot 500SW out of a 2" barrel on moonless nights.
Castle Doctrine or not, I wouldn't shoot someone just for being in my place. Unless it's Dr. No's entry element with SMGs at high ready, I'm probably going to confront a trespasser before decide whether to blast them to the next. Yes, it's a higher standard than the law requires in some places, but if you're technically and tactically proficient, making sure of who you're shooting and why would before executing would be the ethical move.
As for liability, it'd be contingent upon your state law. Whether or not a suppressor is a legitimate aggravating factor in a finding against self-defense is less important than how well an anti-gun prosecutor would argue it to a jury. A good shoot is a good shoot regardless of what's used, but where the law is not perfectly clear there's a lot of gray area for BS to fill up (my old home of Illinois comes to mind, although no silencers there).