Yes they would think. Unless you cut the following dialog:
Piett: Shall I hold them?
Vader: No leave them to me. I will deal with them myself.Clearly they know.
No, Piett is asking because Vader obviously suspects something. Piett "was about to clear them."
Vader knows because he senses Luke. Luke is “endangering the mission.” If Luke wasn’t there, Han & Co. would have sailed right through with no problem.
If you take the shuttle off course then it won’t be clear that Vader senses Luke, and not the shuttle off course.
They knows after Vader makes it clear.