After a very quick scan of the updater source code, I didn’t find any reference to that path… But I can see the same behavior on my device…
So now I have tried deleting the folder and as soon as I have opened the Updater app, the folder was recreated.
Also a funny thing is, that the are creating storage/emulated/0/updater/ AND updater/ in the internal storage 
Debugging the updater is hard because it’s install as a system app that not even TitaniumBackup can uninstall apparently 
Okay, I finally uninstalled the updater with (in the phone shell): mv /system/priv-app/FairphoneUpdater/FairphoneUpdater.apk /system/priv-app/FairphoneUpdater/FairphoneUpdater.apk.bak; sync; reboot
I think I found something… The line final File externalStoragePublicDirectory = Environment.getExternalStoragePublicDirectory(Environment.getExternalStorageDirectory() + resources.getString(R.string.updaterFolder)); gets the path /storage/emulated/0/storage/emulated/0/updater…
I think the programmer didn’t quite understand the method getExternalStoragePublicDirectory (see here for documentation about that method), basically you give it a constant pre-defined like Environment.DIRECTORY_PICTURES and not your own string…
So apparently I fixed it (at least that folder doesn’t get created but I am not 100% the OTA is still working…^^) (btw why am I fixing bugs for Fairphone in my freetime? 
)