They aren't saying Sue was a skrull all along. You saw Johnny say he thought she was still in Vancouver. For all we know at this point, Sue really is still in Vancouver and that skrull only just took her appearance to sneak in while she was gone. Keeping in mind, Sue was one of the heroes to come out of that transport, so we could be looking at 3 different Sue Storms.
Hank Pym is a skrull, but judging by his appearances in Mighty Avengers, I'd say it only just happened recently.
I would definately peg Spider-Woman as being a skrull at this point. She went and called Luke Cage in front of Jarvis and he turned out to be a skrull.