This is a known issue not specific to starmade, but to openGL in general.
Transparent objects like beams and missiles do not render behind other transparent objects unless manually sorted by distance to viewer and rendered in that order.
I recommend using glass for areas where you want to be able to look outside from the interior, while camera blocks belong either directly on the ship's bow or a few blocks back behind an armor layer. Do not use your battle(flight)cam behind glass, even though it seems "logical" to have a cam inside the cockpit.