I have to say, I love having rear access ports. By the time I get home after every sail, my hulls are pretty well dried out. Beyond that, they're great for inspecting the hulls, adding crossbar reinforcement, extra storage space, or my personal favorite: bottleports.
http://www.bottleport.com/Honestly though, I think that's really the best way to dry the hulls out. I think they should've been standard on the Hobie 18. I've heard of some people affixing cowlings to their hull ports when not in use to force air in and vent the hulls. One day I'll figure out how, lol. In the absence of additional hull ports, I think trailering with the ports open and plugs out or blowing fans into the hull is the best bet.
Also, in addition to the leak in the dagger trunk seams, check the hull ports. My boat used to have the pop in style, which leaked horrendously. I replaced them with the screw-in style, but they're still by far my biggest source of water in my hulls, if not the only source. Dry clothing goes into the fat bags, and the come out wet. Murray's sells some better gaskets for them, which I think has helped. I left my boat in the water for a week earlier this summer (sailing most days), and by the end had maybe 1-3 cups of water in one and <1 cup in the other.