Am I correct in thinking that when Innsmouth Horror expansion introduced the 2 aquatic counters for this location (and also River Docks), that this has nothing to do with investigator movement but is only significant for the orange aquatic monsters?

Correct. Except for Silas.

Falcon Point on the IH board allows you to move directly TO there, or move another player FROM there. So it can be an alternate to the train station way of moving between boards. But the more likely effect (and one to watch for) is the movement of aquatic monsters.