I thought that when you spawn NPR with the F9 window and uncheck "spawn with ship systems and designs" they simply cannot have ships because there are no blueprints yet.
I also recently started a new game where I had to spawn 5 different nations, and though I messed the part up for 3 of them, the 2 other ones spawned without anything like they should. It could have been coincidence I guess, but I am doubting it.