I would always go with an external antenna
First, the good news:
A GPS signal will travel through fiberglass
just fine. A plywood
or cored deck
may also let it through, but may not, depending on the thickness and/or composition.
Also, the signals are stronger than they were a few years ago. The signal may bounce around, coming in through windows, etc. A few years ago my Garmin
GPS III+ would not pick up a signal inside at all. But now it gets a lock just fine in the middle of my home office. Don't know if it's coming through the roof or the windows, or maybe both.
Now the caveat:
When mounting below decks, where you will notice the difference is when the weather
is bad or sunspots are active or ... In those conditions, the signal gets marginal. The addition of decks may well make the difference in receiving or not.
I would mount an external antenna if you really want to maximize your reception
in marginal conditions.