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Hmmm... well say you deep cloned it in S3OC, it will come with the effects and it will be possible to do the 'black alpha' trick. TSRW however, does not always show effects. In fact, I even had TSRW deleting my effects, with... well the voodoo doll from the store. And usually in the tab next to 'mesh' (I forgot the name >-<) it doesn't always display the effects. So... TSRW and effects aren't really friends, unless it's an ANIM file.
Though, effects could come within the effect file that's merged together which are called 'VFX'. Then we got the ANIM files, which is more like a GIF but is pretty rare within the game itself. Then there are the effects that are within the bones, like in my reply above. And the last one is the one you're talking about, which is pretty common, but so is the VFX data within the bones, which are then linked with the effects within the SWB file (found in one of the Fullbuild.packages).
So... VFX/effects are basically chained with the bones, because... well unless you want to go into scripting your object to delete the effect, I would just go deleting the FX file within the bones. Or, depending on what kind of effect you got, another way. ^-^