Is it truly an issue? Joking aside its a common bug right now. If you spawn any NPC on your ship their clothes won't spawn with them.
you have really skewed priorities. On your place I'd be freaking over flooded engineering down below. =D
It's for the girl to swim in, she is wearing a bikini after all. Or maybe OP is a Hylotl-in-Training.
I wouldn't exactly call that naked, but whatever. Known bug that NPCs spawned on ships are frequently partial-nudists. At least she's dressed correctly for your pool/engineering room hybrid.