Alright, seems to run again.
I had openGapps pico installed, that seems to have caused the problem.
I downloaded the latest version and (re-)installed it via TWRP, and after the next app optimiztion the phone started again. Only the home screen, i.e. the Fairphone launcher, seems to be broken, so I need to configure it again.
Edit: Launcher problem solved thanks to Titanium Backup :-))
Interesting side note: I also tried to wipe Dalvik & cache in TWRP, which failed. I assume it is because I have the /data partition encrypted. Can someone confirm that the cache is on the /data partition?
I really really hope Fairphone will soon port TWRP 3+, it is really annoying that the current TWRP version cannot handle encrypted /data!! This steals a custom recovery most of its advantages!