So, I was about to start a new playthrough to coincide with the new DLC coming out and noticed that... well I have all the achievements unlocked. Which is wierd since I played through the game only once, meaning I cant possibly have earned the achievements of following the endgame questlines for the factions I did not pick. Anyone else got that weird bug? I can only see the achievements I have completed, there are no greyed out achievements or secret ones being displayed. Should I contact the gog support?

I'd add it as a bug on Obsidian's support forum:
https://forums.obsidian.net/forum/130-pillars-of-eternity-ii-deadfire-technical-support-spoiler-warning/

Include which patch you're on, your OS, whether Galaxy or manual install, and as much info about your PC as possible.
Also, if you can upload your most recent save-game there (not sure if you can upload it to a post - if not, then dropbox or something), that'll help Obs figure it out.