These soft spots are probably somewhat weaker. Lets call it 10% weaker. The layup is overbuilt for most reasonable use. Lets call it 100% overbuilt. Therefore these spots are now 80% overbuilt. i.e. the boat is still stronger than it needs to be.

In other words, it is time to stop obsessing, finish the boat, and go paddling.

Your kayak is beautiful, if you can bring yourself to use it roughly enough for those small spots to make a difference, know that there is going to be a lot of other damage to the boat before those spots fail.