"Jump shock" is more often referred to as "jump blindness", and reflects on it just temporarily disabling sensors and fire controls. However, I think you can still launch self guided missiles and they should still acquire targets without issue. Fighters docked on a carrier do not experience jump blindness if I remember correctly.
Weapon hit shock damage on the other hand is sort of like an incentive to use bigger calibers/warheads. When a large amount of damage is taken from a single missile or energy weapon impact, some extra "shock damage" is added which is applied directly to internal components. The amount of shock damage inflicted is roughly proportional to the damage from the main blast. Note that shock damage does not get applied if the main hit is absorbed by shields, regardless of the strength of the hit.
