Because the nexus mod manager doesn't know if the mod is active or not. All it knows is whether the mod files are in the directory where they're supposed to be.

the mod does have button to deactivate or delete the mod

You mean the nexus mod manager? Yup, that should delete the files from your extensions directory.

Deactivating the mod from your in-game "extensions" directory does not delete the files, but deactivates the mod.

does turn off extension in-game = deactivate mod in nexus mod?
if they are same, then nexus mod is not working properly

Originally posted by kelmenwong:

does turn off extension in-game = deactivate mod in nexus mod?

not exactly.

turn off extension in-game => mod is deactivated, files remain in computer;
turn off mod using nexus mod manager => mod is deactivated, files are not in computer.

turn off mod using nexus mod manager => mod is deactivated, files are not in computer.

isn't this is delete mod?

Ok, sorry, I overly simplified.

When you download a mod with NMM, it downloads the files and places all of your mod files in a central location. (My mods for X:R are in C:\Games\Nexus Mod Manager\X Rebirth\Mods\)

When you install a mod, this is copied to the extensions folder of your installation of X Rebirth. (Mine is in C:\Games\Steam\SteamApps\common\X Rebirth\extensions\)

When you deactivate a mod using NMM, the files in ..\X Rebirth\extensions\ are deleted, however the files in ..\Nexus Mod Manager\X Rebirth\Mods\ are not deleted. (So you could re-activate the mod without re-downloading.

When you delete a mod using NMM, both copies of the mod files (in ..\X Rebirth\extensions\ and in ..\Nexus Mod Manager\X Rebirth\Mods\) are deleted.

.......
And if you deactivate a mod in-game, the mod files are not deleted, but the mod is deactivated.

So, you can either deactivate a mod by using NMM or by using the in-game menu. Both work, but they work differently.

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Personally, I don't use NMM, and prefer to download the files from the Nexus manually. Particularly important for this game, because it's essential to read the mod descriptions, and that's easy to skip when using NMM. Takes more work to keep track of updates, though.