Right Marlen..it affects the integrity of the vessel. It is a huge, dirty messy job to replace the core of a deck and re-lminate. If you have good carpentry and fiberglass skills and time...it is not particularly expensive to do from a materials standpoint. If you need a yard to do it...you are talking about a very labor intensive propositions that may cost a significant portion of what the boat is actually worth.
The above assumes a widespread problem. If it is just a small area, you can just drill holes and inject epoxy for an easy fix.