The achievement now appears to be fixed meaning you need to collect all shelters,
If you see a building with smoke coming from the chimney this will be a safe house. I believe each area has a secondary quest for finding the main hatch for that area however most area have 2 or more hatchs.
Here is the list as it appears in the game.
St. Georges Holm Hatch.
Secondary St georges Holm.
Maidenholm Hatch.
Eel Pie Hatch
Eel Pie Hatch 1
Eel Pie Hatch 2
Barrow Holm Hatch
Luds Holm Hatch
Luds Holm Hatch 2
The Parade.