I always interpreted it as a percentage increase to all damage done by that ship, regardless of type of weapon. It might be limited to just 'fired' weapons, like guns and missiles though (excluding special systems); that would also make sense to me.
Found this on a MoO2 FAQ
. It is for the Mac version, but I don't think that should change how this Leader Bonus works.
"Ordnance Leader Skill
• Works just like High Energy Focus, where the percent bonus equals the
ordnance skill level instead of 50%.
• Works with beams, missiles, torpedoes, and Stellar Converter. Does not
work with Fighters' beams. I'm not sure about bombs (on fighters or
not) or Gyro Destabilizer, Pulsar, etc.
• The ordnance bonus is not increased by Heavy Mount on beams or
Overloaded on torpedoes. Ordnance does not increase dissipation of
beams or Plasma Torpedoes."
Here is a link
to a wiki discussing MoO2 leaders and bonuses in general.