Weapons gone

Not a glitch m8 .
Sounds like they were destroyed during the fight.
Something that heavy radiation can also do, eat up your hull and guns and other equipment.
To be shot off your shield and hull must have suffered badly as well. !

This often happens when your hull is down, and they heavily damage your hull. You will notice that after a fight, you will see a small bar below the initial equipment flashing either green, yellow, orange, or red, this likely assumes it was damaged in a fight. If it is missing, you either didn't buy it, or twas simply shot off in fight. Same goes with Shield, thrusters, and weaponry armaments.

Luckily there is plenty of ship in Crossfire mod (practically all which are not vanilla freelancer ships) which do not have theirs hardpoints exposed so much and is practically guaranteed that you will lose faster whole ships as to lose some of guns. In tough fights you usually lose, at worst, some CD launchers. One from worst ship in "losing guns" regard is vanilla Titan .