If the update notification does not disappear after an update, it is most likely the fault of the modder, as the "version" number in the mod.lua file differs from the "version" in the online database. The modder has to make sure that the version number is correct.
How do you want to check for duplicates? Any mod is identified by it's folder name, so inherently a mod can not be installed twice.
The only possibility for duplicates are mods installed using different folder names, e.g. when using steam workshop. This is a design problem of the complete mod system by urban games in my view. I really don't like the "mod identification" that UG uses (which is in my view non existent ).