Let's think about this for a sec.
When venting, you are removing flux and disabling your turrets and hardpoints for a while.
These turrets and hardpoints require energy to fire their ammunition and have said ammunition leave at a velocity/intensity that will reach and damage the enemy ships.
Missiles, however, do not need to be propelled out of a tube as they have their own form of propulsion.
Whilst it is advantageous to have the missiles shunted out of their racks/tubes/pods and already be moving at a velocity, thus not requiring fuel to launch and giving them more range, the constant use of this effect could cause wear and tear on the ships. (think of the damage caused to the pod/rack/tube by the flaming exhaust of the missile)
So, I propose that the captains, knowing of the effects of these missiles, would coat the missile launch bays in some form of flame protectant to reduce this damage cause by missiles launching while venting. However, the missiles use up a significant amount of fuel in their takeoff phase and also leave the ship at a lower velocity.
TL;DR If you launch a missile while venting, it should have a lower initial speed or take longer to reach max speed and it should have a lower range (70-80%)