The turrets are all manned, IIRC; so they don't go down when you kill the computer. They just lose enhancements like target acquisition.
I wouldn't say "only" to that: missing th target aquisitions mens no target identifier and no pips, so basically the tuttert operator will be shooting just by eye sight, and in space that is extreamly hard to do, plus the chance to shoot one of your own.
Bringing down the turret target aquisition will prove a good adantage for the attacker IMHO.
I just took a moment to google how to build shielded EMP electronics, couldn't find much as Google just tries to sell me junk these days, but what I did find suggests when electronics are built to withstand EMP it's designed into the circuits from the get-go.
What is the range of a current ship EMP? How strong an EMP do you need to offline Capital Class components? Will a milspec ship have systems designed to mitigate this kind of risk from the ground-up to render such tactics a low risk anyway?
Is there a chance a ship-bound EMP from a Warlock or Sentinel won't have enough throw to cover a whole Idris at once? If a warship is anything like the Vanguard it'll have backup systems throughout the ship so even if a third of the ship is effected by something like an EMP there will still be components in the unaffected parts covering that job...?
Also, being military, would there not be some clever system to receive the incoming energy and store it in the ships capacitors to use in its energy weapons and other systems? I mean, you have a bubble of energy surrounding the ship in the form of its shields. If we can suspend energy in place like that can we not also catch and collect it given the right onboard ships systems?
How many times can I write the letters EMP in this post?
Good point, I'll expect that military grade components have some sort of build-in EMP resistance in the future, but most of the shielding I think will came from the add-oon you can install in each component.
CIG talk about it in some video several month ago and form the description (subject to chance of course), the right add-on can provide a good protection against EMP attack, and in a capital ship, where component are reduntant and there are personal for theyr mantenance on the spot I'll expct these to be very resistant to EMP attack.