I just noticed not only is the description for 'Überwachte Ordner' but also for 'mod-speicher' twice. Not the same wording, but it seems like the final formulation is mixed with the draft.

Under 'mod-speicher' delete:
'Wo Steam Mods gespeichert werden sollen:'

Under 'überwachte ordner' delete:
'Wählen Sie Verzeichnisse aus, die Arma 3 Mods (Mod-Verzeichnisse) beinhalten. Erkannte Mods werden automatisch auf der "MODS"-Seite angezeigt.'
'Kürzlich hinzugefügte Mods werden durch ein automatisch hinzugefügtes Label gekennzeichnet.Erkannte Mods werden automatisch auf der "MODS"-Seite aufgeführt.'

The problem here is the Arma 3 Launcher.
In the launcher settings under 'mod options' is the feature 'mod storage'. The description says it 'will also move all the mods (...) to this folder.' By default its set to the Arma 3 folder and you cant disable it!
BIS has failed to think even the slightest about the consequences of this 'feature'.

The intention for this might have been the unclear names in \SteamApps\workshop\ or to arrange all your mods neatly in the Arma 3 folder.
Steam can fix both of these problems.
BIS cant without creating more severe problems. (double the size, manual deleting + unsubscibe -> no auto updates)

In my opinion both initial problems are solved with the mod overview in the Arma 3 launcher.

So the solution is to delete this 'mod storage'-shit. And if BIS does so, please make a popup on next launcher start, to delete the made copies as a lot of people dont know about this.