Why are they used so infrequently?

I would guess that for the fences like the ones used on the Mig the interference drag might be the killer. The fences were not tall, but they're pure interference from front to back and that's both sides of the fence. And from their front to back layout they'd be almost impossible to install cleanly. And for long term maintenance of a wing would be in the way of just about half the components that might require access.

We can more easily place fences on models and do it "slicker" and it won't get in the way of our maintenance men. Airlines and airforces won't see any positives about them.