First, about water getting into the open plugs. There are two ways to handle this. One is to run out to the boat everytime it might get wet or snowed on and replace them. The second option is to store the boat with the bows slightly higher than the sterns. This will prevent water from getting into the hulls. I don't bother with either way. The amount of water that will get into your hulls through the drain plugs is minimal unless the storage location floods deep enough to submerge them. I have stored both of my boats like this for years and the hulls are dry in the spring.
Don't forget as the air cools it can hold less moisture so the water condeses out. This will introduce water into the hulls "that wasn't there". Good air circulation will clear this condesation out better.
Now, strong winds and Hobies on trailers. I lived in northern Indiana for about 16 years and had my H16 for the last 3 I was there. I went trhough many tornadoes and strong summer storms. I never tied my trailer or boat down and it never blew over or across anything. I was probably lucky. If you are worried about stong winds in the winter I would remove the tramp (I do this for winter storage no matter how windy it is supposed to get) to lessen the "sail area". Keep the boat tied to the trailer and you should be fine. If you are still worried about it, go to Pet-Co or some other pet supply store and buy 4 of the corkscrew dog tie downs. These will work great. I use them to tie down small airplanes when I fly them into the back country and have to leave them for a few days. If 3 of them can hold a 3600 lb flying machine in place I think 4 will sufficiently hold a Hobie in place.