In general it's OK to uninstall them. You should look at the mod thread or any instructions that came with the mod and see if it says anything about uninstalling, or follow the installation instructions in reverse if it doesn't (for example, if it says to upload files to install a mod, then it's probably a good idea to delete them from your server if you uninstall it).
If you plan to use a mod again, that might be a different story. If the mod saves data in the database then you might want to disable it instead of uninstalling so that you don't lose that data.
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