See the bugs listed on this wiki page. Apparently weapons can fall down, disappear, move etc using weapon racks.
Even a bigger problem, the staff of magus is a known bugged item on weapon racks.
If you are playing on the pc, there are some dodgy solutions, but they focus more on weapon racks that are not usable, not the disappearing weapons.
You could use the no clipping mode. (open console '~', type in 'tlc' close console). And walk through the walls to look for it.
Or you could spawn a new staff of magus using a console command. In the console type in 'player.additem ITEM "00035369"'. You should have a new staff of magus in your inventory. (00035369 is the item code for the staff)