Yes, you can remove them. I highly recommend you keep the zip of the current ROM you're running. I say this because a lot of issues you may end up having (bad mod flash, etc.) can be fixed by just reflashing the zip of your current ROM. Of course, a nandroid backup will work too, but this way, you don't have to lose data/settings since the nandroid backup. You will have to reapply all mods, but that's generally not a huge deal. You, of course, can remove the zip, if you want, though. The running ROM uses it in no way whatsoever once it has been flashed.