Ha Bottomline
If you are running a outboard you should be ok to fill them up but is you are a I/O or Inboard guy I would leave them in. If you are using a outboard your only concern is for gas fumes from the tank not the motor which can be vented from under the center consol by placing a vent there or from under the cap by placing 2 two inch diameter vents on either side of the transom area above the storage boxes or there about. That is a simple glass job remove the vents epoxy backing behind and then fill in with glass resin and paint or gelcoat to match.
http://www.classicseacraft.com/mcgovern23page3.htm
FellowShip [img]/images/graemlins/grin.gif[/img]