Just want to reply to this thread as I resolved it on my own.
Unfortunately the only way was a Full-Wipe (Dalvik / ART Cache, System, Cache, Data). Of course a backup of your data should be done in advance. (I used oandbackup, contacts+calender were synced via DavDroid with my mail-provider, you should save your pictures and other file which don’t belong to a specific app separately). So after the wipe I flashed the Fairphone Open 17.09.3 via fastboot and setup/recovered all my stuff step by step / from scratch. Annoying and time consuming, but at least everything is fine now again. Good to know that all the restore and sync stuff worked as expected.
I assume that most problems had something todo with the Snooperstopper issue I already linked in my first post.
Solving this one I used a TWRP-backup of my encrypted phone after I had to wipe the system completely as well (I thought this is ok as TWRP de-cryptes the device directly after the start and before performing a backup). Unfortunately as you could read not everything worked after that (and I recognized not everything directly). I think most of the issues were related to that. Eventually the Yalp Store problem was just a missing rule for the Downloader in Afwall+.