Heya,
I’m not sure (I don’t own them), but I think the the Wondertouch emitter presets (and related media) were installed in the Motion Library path, which was in /Users/Shared/Motion/ in Motion 2.0.
As of the new version, all of Final Cut Studio seems to share a common content library path, which seems to be /Library/Applications Support/Final Cut Studio/.
I’d contact Wondertouch and ask them the proper way to relocate/reinstall the emitter presets is so that they’ll show up in the new library location. They’re just presets and images, so they should be compatible with Motion 3.