Yes, it's most likely that the "match" function ruined your library in Music / iTunes (I'll call it iTunes for simplicity), but it could also be due to a couple of simple check-boxes in the preferences... one which allows iTunes to manage your files, and another which copies the music to the Music folder when you import music to iTunes. Those two simple boxes can destroy a collection without any effort.
My suggestion is don't use iTunes. I personally use it to facilitate the transfer of music to my iPhone, but that's it. Everything else in my rekordbox collection is added directly there, with the music being managed on my hard drive myself. I use a series of folders to organize it by source and date. All the rest of the sorting and management is done within rekordbox.
I've done away with the archaic Artist / Album / Track structure within the software, that is only important if I want to browse the songs on my drive in that manner, and is still available in rekordbox should I choose, but I don't make any effort to do that with songs downloaded digitally from other sources (like Beatport).
Spend the time sorting your music properly before it ever gets to software and you're set up for success.