Starsector 0.97a is out! (02/02/24); New blog post: Simulator Enhancements (03/13/24)
Your stations arm themselves using the weapons you have blueprints for, and the player only starts with mining lasers and blasters for energy weapons.If you get some new weapon blueprints and prioritize them, your station will refit it's weapons accordingly.
Unfortunately not. You also cannot manually alter their loadouts, which is both a code limitation and by design.