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Are they in your server's maps folder or in the downloaded maps folder? I know that the CS maps are there because CS:S is mounted, but I don't know about those Koth and DOD maps.
From my experience regarding extra maps, they're not a huge problem. Just make sure that, if you're running a Jailbreak server, you do not allow any users access to "ulx votemap2" or they'll be able to vote for them.