I believe PvE and PvP should have the same rules applied to Claims/Settlements/Tax I also think Wars should be possible on a settlement in PvE just like in PvP with one exception, both parties approve the War or an allow war check box for settlements in PvE. Maybe people in PvE would like the War aspect but prefer to be safe sailing the seas compared to PvP style anarchy.
Several of our company ships have had beds vanish. When you try to spawn on the beds for that ship the list will show all the beds you placed, however if you select one of the beds that have vanished you will get a green map and not spawn to it. Makes it very difficult to spawn on ship beds, specially if you can't tell what bed is still working.