Is it possible for an engine to be stronger at short time controls, and weaker at long time controls? Is it possible for engine A to be decisively better than engine B at short time controls (say, 5 min/game) but decisively weaker at long time controls (say, 1 hour/game)?

If the answer is yes, what could possibly be the source of the discrepancy? If the answer is no, why do we need long time control tournaments like the TCEC superfinal, when we could just get both engines to play each other at short time control much more often?
Why not? I don't have an example here, but cache implementation could be a major factor.

A cache algorithm that doesn't scale well with time will not perform well on a long time control. No matter how much memory you have, at longer control it will surely be filled up very easily and very quickly.