I use my kayaks very hard, and like to add a little from my experience to the above.

Superficial scratches in the varnish coats is a minor problem - easily touched up. But often a scratch dislocates the individual glass filaments in the fiber bundles, breaking the epoxy-glass bond and exposing light reflecting surfaces within the glass layer. Those scratches appear white due to light reflections and are impossible to fix nicely (short of refinishing the hull - epoxy, glass and all) - impossible to force epoxy back into the bundles and of course no use with an extra layer of epoxy or varnish on top. The only functionally efficient measure is to replace the damaged glass-epoxy layer - which of course leaves a lighter colored area that takes years to blend in with the rest.

An extra layer of glass protects the wood and is therefore a sound idea, but does not help against those deeper scratches, and more layers than that may be counterproductive, reducing the flexibility of the glass layer and may cause delamination after hitting a rock.

So for kayaks that like mine are used hard, there are a few advantages with a painted or graphite coated bottom. And when painted it is a good idea to use pigmented epoxy from the wood and up - keeps the inevitable scratches almost invisible...