You can reimport over your existing ones, yes. If you use the same import directory/structure, it’ll just recreate the UE materials and texture files.
You’ll have to manage your multiple copies yourself if you import to other directories (although HammUEr should always use the latest imported one), I’m afraid.
I’m pretty sure if you’ve saved a map in UE and try to reopen it after deleting its original materials directory, it won’t be able to find them… but I haven’t really tried that myself.