1) Intimidation factor - a handgun at thirty feet, especially in a dark house, doesn't look terribly threatening. Even if the intruder recognizes that you have a gun he probably isn't going to be able to distinguish a Desert Eagle from a target .22. Chambering a round on shotgun makes a noise that will get almost anyone's attention.
2) Number 4 buckshot has 21 pellets is a standard load versus one bullet per round in your .44 Magnum. I'm glad to say that I don't speak from experience but I suspect that accuracy on the range does not transfer 100% to actually shooting at a person, especially a moving one. At interior distances a shotgun isn't going to be spraying pellets all over but you will have a much larger diameter impact zone than a handgun round.
3) Most handguns, especially .44 or .357 magnums, have severe problems with over penetration. You don't want to take the risk of shooting your neighbor or someone from your household two or three rooms away. Your handgun only will cause less damage if you hit the guy squarely in the upper torso. Under many other scenarios it can cause far more damage than a shotgun loaded with #4 buck. If you have real concerns get a dog and an alarm system or move. Deterrence is always the best defense. Noting how well the average person drives a gun wielding general population is not going me feel more secure.
