Is there any disadvantage to running a long cage mech with a smaller cassette? Or should I go to the trouble of changing the mech back to the short cage?
Not really. Only thing I can think of is the 'crispness' of the shifting might be affected a little. Personally, I wouldn't bother changing unless aesthetics are really really really important to you.
I'd agree with arriere, I doubt you would notice the difference.
Long cage is normally required with a triple, regardless of cassette.