Hmm, 1000 files are a bit much, but nothing a 64 bit computer can't handle.
There is no hard limit within reason I'm aware of. Maybe 65536, but the download list control would probably break down before that.
I'm also not aware of any "conversion" required. Just opening them should be fine. The "importer" is very obsolete and meant for importing from clients nobody probably uses anymore. If eMule was shut down cleanly last time the part files should not even require a rehash. (Rehash is done when timestamp of .part and .part.met differ. It requires reading the whole .part, but happens in a background thread.)
Anyway any performance issues should depend on the number of partfiles present, and also their total size. There is no "adding" that takes extra performance.
If aMule hangs on startup take a look at its logfile where it hangs. Logfile is in C:\Users\YourName\AppData\Roaming\aMule\logfile .