Sure. Run it as often as needed. It may block bayes access while it is running, so if you have a really busy system (and it sounds like you do) you want to run it often enough to keep the processing time for each shot down to something reasonable.
Strange thing is that its not a very busy system. Its a small business mailserver with about half a dozen users (most of whom don't get much spam - we get about 30 spams per day). I use FuzzyOcrPlugin, which probably slows things down a fair bit.
