Plywood is better where there is compressability issues like under
mast steps or where
hardware like winches could be expected to be mounted. Unfortunately, it's more prone to large area
rot problems should there be a leak. The
water wicks along the grain of the
wood eventually rotting over larger areas. Plywood is also much heavier so it counteracts, somewhat, the weight of the
keel if used in the
deck.
Balsa
core is vertical grain so water intrusion is more likely to stay localized.
Rot will spread more slowly as the water largely only migrates as the cellulose in the vertical grain cell walls break down from rot. Balsa core is pretty stiff but is compressable so needs
backing plates, the larger the better within reason, to spread the
compression loads and an easy hand tightening down fasteners. Balsa core is way lighter than plywood which makes for a stiffer
boat though that's probably only a really significant issue for racers.
Given my druthers, I'd opt for balsa core but would install all the
hardware my self. Essentially what I've done on my new, to me,
boat. The core hasn't been an issue. My previous boat is going on 40 years old with a plywood core and is doing just fine. Of course, I installed most all the hardware on that boat and the subsequent owners were equally as careful with what they added to the
deck.
Foam cores don't have rot problems but other issues. The biggest one is breaking down of the surface of the foam so the
fiberglass laminate is no longer adhered to the foam. Negates the 'I' beam stiffening effect of having the core with the inner and outer FRP layups. Foam is also compressable though don't know whether more or less than Balsa.
Non cored frp layups have very low stiffness so need reinforcing at regular intervals. Not so serious with a
hull as the loads are spread over larger areas. Still, many FRP
boats used glassed in grid systems and/or laminate the
interior furniture to the
hull to give added stiffness. On a deck, the reinforcing grid has to be at much more frequent intervals as the point loads are way higher unless you only sail with 100lb models and stay at the
wheel ordering your harem about. You can add stiffness by increasing the laminate thickness but it's a very heavy and inefficient way to add rigidity to a laminate.