In the US, will the tower likely think my aircraft has been hijacked if I taxi with the flaps down?
will the tower likely think my aircraft has been hijacked if I taxi with the flaps down?

No.
For the twenty-some-odd years I owned my plane, I only taxied with the flaps down (for important operational reasons), even at towered airports, and not once had anyone think I was being hijacked.
Indeed, it would be quite disconcerting (to say the least) for ATC to treat any behavior or condition not officially designated for the purpose as a signal that the aircraft has been hijacked.
For many airplane types, there are of course good reason not to leave the flaps down while taxiing. But worrying that ATC will think you've been hijacked isn't one of them.