I customize a lot of FS9 effects, and in the course of my labors, I've noticed this: (Stay with me) You can make changes to aircraft.cfg files with the sim running. All you have to do is reload that aircraft in the sim to see the changes you've made. Not so with effects. If you modify an effect, you need to shut down and restart the sim in order to see changes to that effect file. This suggests that the sim must load all the effects in the effects folder on startup.
Now, with more than 85 gigs worth of aircraft in my hanger (and all the corresponding effects that go along with them), it's no surprise that my sim takes almost a full minute to load.

Although it may seem like it hangs at the splash screen, I would suggest waiting it out. Obviously you shouldn't need to wait for more than a few minutes depending on you system's specs, but give it a chance.

Well...it shouldn't take bours I wouldn't think, but 3,300 effect are an awful lot to load.

Just out of curiosity, what made you decide to do this, and the new effects are all for FS9, right?