It should contain loot according to the UESP wiki, so why was it empty? :/

Some times there are small glitches in the game; that or something didn't load correctly.

Wait, it's supposed to have loot? That thing's always empty in my games!

It isn't a loot chest. It is used by a script that cleans up the room before the boss fight, so should be empty unless you dropped something there beforehand

That's quite right; as far as I can tell, your intended "loot" is on Harkon's corpse and that's that.