"You took Hook's ship to Neverland?" There had been other pirates around the place from time to time, but with the way things seem to be working, there are no coincidences even if seems like there are, and Hook would be the most accidentally-coincidental of them to show up. Plus it makes sense that Hook would make an effort to show up wherever his father is.

It doesn't cross his mind that maybe his father doesn't realize he knows Hook, nor does he stop to wonder how they knew how to sail his ship. He went, apparently, and he would know how.