This will be short because it's very simple.
FreeSpace 2's damage scaling makes it impossible for light weaponry to destroy ships with the "big damage" flag. Adding a "huge" flag to a weapon will solve this problem, but then the AI won't use it against fighters! Fortunately, there is a solution.
By giving a weapon $Substitute with an period of 1, you can replace all of its shots with another weapon. This is significant because it allows small ships to utilize weapons with the "big ship" flag. It can also be used to bypass engine restrictions so that the AI will target fighters with "huge" weapons.
Either of these flags allow a weapon to destroy warships with the "big damage" flag.
Ignore this crap. It's wrong and AI fighters will fire huge primaries without any extra measures.