What could cause lower torque than normal during cruise in a King Air 300?
My guess, and it's just a wild guess, is humidity based ice forming somewhere in the inlet and/or the inlet plenum, more or less similar to carburetor icing.  The symmetrical torque drop is from the flow restriction and the random vibration is when the ice breaks up. I'll guess that you were flying though what appeared to be clear or clearish air with the inlet/plenum anti-ice turned off.

Double simultaneous random mechanical malfunctions are just too microscopic from a probability perspective to be likely at all.  A phenomenon like that, that happens to both engines at the same time,  must be due to an external source related to the atmosphere the aircraft is flying through, unless there is some other system on board that impacts both engines equally if it malfunctions, and that's something you won't generally see design wise.

I would try this question on PPrune Forums.  Somewhere there is a King Air or Twin Otter driver that's had the same experience.