To me, the advantages of a handgun for home defense are that it can be used one handed if needed and it's easier to keep on your person at all times within the house. Obviously, long arms can be more powerful than handguns and are usually easier to shoot accurately.
My long guns are locked in the safe but I can keep my EDC with me in the house. If I had plenty of advanced warning, I'd barricade the family and get a long gun out after calling 911 for help. If I had time to do all those things, I should have time to put on some hearing protection.
For folks that want to use a 5.56/.223 type firearm for home defense, they could minimize muzzle blast and flash by careful choice of ammunition and the use of a flash suppressor rather than a muzzle brake.
This chart indicates that an AR with some muzzle brakes is more than ten times louder than the same gun fired with the quietest flash suppressor. Even the inexpensive A2 flash suppressor is less loud than any muzzle brake tested. Muzzle brakes may help a little in competition but I don't see the point in one on a home defense rifle when a flash suppressor not only reduces the muzzle flash, it is less loud.