To answer my own question, it appears that one of the streaming sites I tested (abc iview) tried to load plugins (drm). This messed with the config and voila, webgl stopped working.

Copy /usr/share/sailfish-browser/data/prefs.js to .mozilla/mozembed and you are good to go. I kept a copy of the old prefs file, so when I have a bit more time, I'll diff them and find out what went wrong.