the beam direction doesn't update like it does if you manually fire that beam and hold the mouse button.

What you get is similar as if you pressed the mouse button once every logic cycle (0.5 - 1 second). The beam will stay aimed to a point so if the ship rotates the beam will not rotate with it till you fire again.

A logic activated weapon should be the equivalent of "click and hold mouse button" for the duration of that weapon's burst time.