I've walled in NPCs any way I could imagine. It's never stopped them from suddenly not existing, except the one in my Floran's ship.
hm, that's quite odd.
I do hope that doesn't happen when I set it up. Maybe I'll just build my base and leave it empty until later updates.
EDIT: Progress

pretty low on resources, but getting soft stone bricks and light metal is really tedious and difficult
additionally, I am now monkeybird