I had the following problem and am posting a solution to help others.
After installing STO and playing for a week, my computer began to run its hard drive constantly. I checked the performance monitor and discovered that Vista's SuperFetch preloader was accessing the huge .hogg files in STO.
I simply went to Control Panel | Admin Tools | Services and stopped the service, then used properties to disable it.
My problem ended.
My research and experience so far is that SuperFetch is of dubious value with under 4GB of RAM anyway, and nearly worthless to gamers.
Ironically, SuperFetch only became a problem when Vista realized STO was the only program I was running! So, if you are a more balanced person than I, you'll probably be ok.