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.
I see what you’re sayin’, but I don’t think Vader sensing Luke would get lost if this change was made. It might change what initially alerts Vader, but the audience would still realize that he knows Luke is on board through the already existing visuals, editing and the direct dialog that says so.