The fiberglass on our boats has 2 layers: a glass-impregnated-with-epoxy layer (known commonly as the 'glass') and gelcoat (that shiny colored part that you see). The glass provides you strength, but is not waterproof. In fact, water can migrate along the little microholes in the glass (known as 'wicking'). Now, not enough water will get in for you to even notice. However, enough water can wick through the glass so that it can get any wood embedded within the glass wet, causing it to rot. Now, I hasten to add, Yamahas have very little wood, but some of them do have wood used to add more structural stability, particularly at the aft.
Gelcoat is the waterproof part. But gelcoat is not strong/structural. In fact, it can be rather brittle, which is why it may chip if it gets hit. Any chip, gouge, scratch that does not make it down to the glass is not critical. You can fix that with a little Spectrum color-matched gelcoat (they sell a paste in a little jar--magic stuff). But if you do not do so until next season, it is no big deal.
If you have a chip that goes through and exposes the glass, some will say that needs to be covered immediately (and there are temporary epoxies for this purpose). I think it depends mostly on how big the problem is. If you look inside your hull, the raw glass is there and if any water gets into the bilge, certainly some of that wicks into the glass. So a little chip or nick down to the glass I personally don't worry about too much. Fix it in the off season. Bigger than a dollar bill? Nope, that needs to come out of the water and not go back in until it is fixed. Not only do you have water wicking to worry about, but also structural integrity and additional damage to that gelcoat around it.
Do note, however, that this is only for Yamahas. Other boats use much more wood, gelcoat or seal the inside, etc. in their construction. On one of those your little nick can cause a big problem if not addressed promptly.
