The weird thing there is that we saw Hank's *thoughts* back when he was dating Tigra, and he was very clearly not a Skrull, and then, bang, retcon, he was a Skrull! Please ignore that the writer didn't know it, and thought he was writing the real Hank Pym...
And that could be the No-Prize winner to the 'why didn't Tigra's empathy pick him up?' if Skrull-Pym was a Manchurian Candidate, and has been psychically conditioned to think he was the actual Hank Pym, until a trigger phrase or event or whatever snapped him out of it and restored his original Skrull memories.
Plus whatever the Skrulls were using for these deep cover infiltrators was supposedly able to fool Dr. Strange's magic and Xavier's telepathy, as well as any machine-testing that Stark or Richards could come up with, so it was kind of a buttpull/mcguffin-of-unobtainium plot convenience already. I could probably come up with some explanations for how their alien super-science could trick human genius-science, or even Manchurian candidating could fool telepaths (and empaths), and just a faithful-to-the-role diet and such could deal with enhanced scent (probably the easiest thing for Skrulls to deal with, with millenia of experience at pretending to be other peeps, around all sorts of other races, at least some of whom, like Mephitisoids, have enhanced senses of smell), but *magic?* Sorcerer-Supreme-level magic?
That's just bad writing, as Deadpool says.