I also don’t think it would get too lost either. Even when you watch the scene, I don’t think right away the audience think “Vader knows Luke is there” when he asks about the shuttle. It seems RIGHT at that moment the thinking was more like “there is a shuttle that came from no where and wants to go to planet, that seems a bit odd.” Hence, why he wants to know what that shuttle is doing. Once he begins focusing on the shuttle, then he sensed Luke’s presence.

Or, one could think he felt something was off about the shuttle and wanted to explore his “gut” feeling. (force, whatever.) It was then confirmed later in that scene.

From the scene at least, it wasn’t until the dialogue a bit after his question about the shuttle it was implying Vader was sensing Luke specifically. SO adding more shuttles in the scene or whatever does not affect the dialogue at all.