I've removed my stock side scoops a couple of times lately, because I temporarily installed the Bullitt side scoops.
If your 2000 is anything like my 2002, then there are lots of holes, and one very large hole (several inches wide) underneath.
I was not happy with the way the Bullitt side scoops fit, and the fact that you have to use 2-sided tape or epoxy or something because they have no attachments in the front. Also, the 2-sided tape did not seem to be working well on one of them, so I removed it, and the next day the scoop flew off, so I threw away the other one as well.
So now I have the stock side scoops on again.
I will probably just remove the stock side scoops, but this time cover the holes with fiberglass resin, sand the fiberglass resin, and then paint it or get a body shop to paint it.
The stock side scoops on my 2002 were fairly easy to remove. I just pulled hard on them and they popped off. However, I did damage some of the rear attachments on one of them, but I was still able to re-attach it later.