One solution for this is to have your spaceship actually static in terms of position, and have your controls actually move all the other objects around it and rotate the entire layout.
Another involves setting up a custom pathfinding system that allows for node positions to be pinned/updated with movement of your ship. This can be done in conjunction with the built in pathfinding behavior, as that allows you to access the node coordinates. Basically use the pathfinding behavior to calculate the path, then your own movement system by creating invisible helper objects at each node that are pinned to the ship, and have your NPC's ( which are also pinned to the ship) move towards each node object in succession.
Third way is just to recalculate pathfinding every tick. Definitely not recommended, unless the scope of your game is very, very, small.