Do I score fishermen for settlements on water?
No. For scoring the Fishermen card, you can ignore any settlement on a water hex, no matter if it’s adjacent to another water hex or not.

From the rules about the Fishermen card (page 5):


  Note - Extra harbor action:
  The "Fishermen" card does not generate
  gold for settlements on water hexes.


This is also part of BoardGameGeek’s Kingdom Builder FAQ: Fishermen: no points for settlements on water hexes