Yeah, Rosenberg really misdirected the fans with that one. He kept going back and forth on whether she would appear at all, but this was a good showing, and the way it ended implied that she and Bucky, at least, might be back.
We don't know what happened during the 45 minutes spoilers:end of spoilers
the team spent chasing Ronin, and it's possible that it was all action and no time for conversation, so I can buy that she didn't catch on right away. Plus, it's been a few years, and she's probably not on as high a guard against Skrulls as she was back then. I think that she and Bucky might be able to piece together that it was a Skrull, but even if they do, that doesn't mean they'll realize that the Skrull had Clint's permission to impersonate him. It could be funny if they came to some other conclusion which leads to a misunderstanding and some shenanigans.