Some people/places like everything to be schematic driven. That way the only changes to the design come from one guy/department. So even though you could add mounting holes in layout and connect them to a net, you put them on the schematic instead. That way you don't have to rely on a note to the layout guy to "add four holes and connect them to GND net". You may also have a bunch of predefined holes and you want to make sure that version gets into your layout.
In the case where you are not connecting the holes to any net then you might want to make a mounting hole as a mechanical part (no nets), just so when you push from schematic to layout the mounting holes automatically get pulled in. This is useful not just for board mounting holes but also for say a heat-sink that goes with an IC.
Really it's just a way not to forget about them or to make sure the right holes are associated with the part or board. You might make the decision on what holes to use well before you get into layout so why force yourself to remember. Especially when your boss is screaming at you to get it released :)