I agree with Mideast in saying they are very common, but almost never used to scam people, at least when talking about NES and SNES. In my experience, sellers are very up front about repro boxes or at least include the info in the description. I'm not sure if this is because repros are easy to spot once obtained or if there is some small sliver of ethical conduct left in this world.
I purchased about 1000 NES & SNES boxes over the past five years and only received unadvertised repros once or twice. One was a copy of FF3 and the other was Rambo for NES, which remains debatable (ink and detail were accurate, but cardboard was white; there are some reports of early Acclaim games with white cardboard, but has never been confirmed).