Well, it may seem unsavoury to you, but respecting the likes of Dr. Light and other villians of a similar caliber would not be very high on my to-do list
And I mean, it's not like they're going to throw the bodies together in one big pile in their basement
The way I envision this would be sort of like a morgue where each body has its own little pull out shelf with their name and information inscribed on the outside of it. Pretty much the same as a normal graveyard except: 1.) no pretty headstones 2.) much more easier to monitor and guard