Secret passages that aren't always accessible, mind you, but that can only be entered for a short period every few decades. Most likely following a particularly strong Aqua Laguna that lowers the water level enough for the caves to be found and sailed into.
Hey, hey, hey, since I was able to draw your attention with this (though we both know that I didn't leave it out intentionally but by accident^^) you might aswell add your the sketch you did to graphically explain your theory. Come on, now that I've said it people are aware of it anyway. ;P
Btw, I'm not so sure about the every few decades thing anymore, since one of my more freakish theories invovles that now Crocus can get to Raftel whenever he wants.