EDIT: Even after supposedly patching the achievement this is still bugged for a lot of people but I'd like to just add in a possible solution from the comments by Luna go sky:
For everyone who unlock every hatch and and the achievement is still blocked, you need to start a new game from zero and open every shelter again. In my case the achievement pops after the third shelter located in Maidenholm.Original "Solution" Below:
I'm not 100% sure if I got this unlocking early, or if it only counts those particular ones, but I unlocked this achievement while still having four shelters still listed as "unknown".
The first thing I did in each new area was to unlock the shelter (as I'm sure most players do) and this achievement popped for me in St. George's Holm.
Not sure if it matters which one in St. George's Holm as there are two in that area, at the time of writing this when I go to travel the list shows as:
St. George's Holm
Eel Pie Holm