I like what you are saying and it does seem odd that some systems are immune from damage - I can shoot off all the guns on your ships but not the launch tubes for your missiles (seekers) or your close defense guns (anti-fighter batteries), but would you not have to reduce the cost of the various systems to take into account the fact that they can now be damaged?

If my countermeasures used to work for the whole of the battle (well, until the ship is destroyed anyway) but now only work for a proportion of the battle based on hull size and the number of other special systems on the ship I would want a proportional reduction in the cost of the system.

I really should read the books I have....

Looking at the Critical Damage rule in the Annex, it seems rather odd that for some systems (Marines, Mines, Teleporters) you roll once per point, but for Anti-Fighter Batteries you roll once for the whole lot, no matter how many you have.

Surely these should be rolled for individually as well?

The Starmada "X" Version of the game had these systems get hit on a certain roll of the dice, the same as all other items such as weapons, shields, engines, etc. 
I have a suggestion to put into the Starmada Admiralty version to deal with this.  Perthaps these could be added to the weapons; they could be damaged as if they were one more battery.  Often for my ships and the ships of others I game with, when you roll a 5 or 6, then roll a second dice to see which battery is hit, often only a 1, 2, or 3 actually gets a weapon hit.  4, 5, 6 are usually misses.  This could be where these Special Equiptment is hit.  Make them as if they are another battery, call it Battery "S" for Special Equiptment.  The more items there, the more the "S" battery appears on the reroll that occurs after a 5 or 6.
That would allow these special items to be hit, but not require a Big Change to the wonderful Admiralty Edition rules. 8-)
What does everyone else think about this change?  It could be an option added to a shipbuilder program.