Aaronhoy,
I am a little uncertain regarding this part of your question:
"if your hull was so well sealed that pressure was equalizing then it would never take on enough water for this to be an issue".
But, since I have the time today, I will try and cover all the obvious angles on this.
With regard to a perfectly sealed hull being unable to take on any water, I would have to say you are perfectly correct. However, as ambient temperatures rise and fall and the internal temperature of your hulls change, you can expect significant changes with the internal pressures of the hulls as well. These could be greatly enhanced or inhibited by the effects of cool water or the radiant effects hot sunshine. Those experiencing the aforementioned "swoosh" are subject to this situation. Although I cannot comment on the particular strength of the H16, I can say this could be very bad. It certainly could accelerate a delamination process (especially in a cored layup construction) and possibly even crack open a hull. The concern over a "perfectly sealed" hull then becomes an issue of damage from pressure as opposed to water.
I believe the Hobie techs could address this much better than I can, but it seems pretty straight forward to me. If the architechs and builders of the hull wanted it truly air-tight, they could have done it in the factory with relative ease. The real trick appears to be how does one significantly minimize water accumulation while maintaining good pressure equalization...again, not a tough thing to do. This is even easier than creating an air-tight hull. But, sealing the pylons (vents) would not be a good idea at all - in my opinion. If you are trying to find some special point where the hulls just barely leak air (equalize) yet somehow completely inhibit water intrusion, I would have to say it is not a realistic goal. The best you can hope for is to plug all leak points on the fiberglass hull itself and be sure that the foam plugs in the pylon are in good firm condition so that they cannot simply act as funnels for water to enter the hulls.
Dave