It runs perfectly. 60 FPS stable. I only just started a new playthrough so how performance is late game I don't know.
There is no community control scheme for it so I'm working on that. I'm using the right track pad as the mouse, left track pad as the mouse wheel, left trigger to select enemies in combat, R1 and R2 for two different weapon groups and the back paddles for things like transverse jump, scan etc. Left thumb stick as WASD.
Unless Fractal launches Starsector onto steam it won't be supported but as there's a Linux version it really doesn't matter.
This took me some time to figure out so for future people I'll add this, to add it to the steam deck UI all you do is launch Steam in desktop mode (not the Steam deck UI) and add a non-steam game just like you would on a desktop, and point it to starsector.sh.
Edit: Combat, moving and shooting is very playable but sadly the moment opposing ships meet and start firing the game freezes and I don't know why. No mods installed.
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