@AlanT is correct this is The Ethos Effect by L E Modesitt Jr, and I'll be awarding him the correct answer rep, but I wanted to add some extra information after googling the book. I wanted to be certain that this was the right book and felt that this could help other users in future (perhaps) after finding some of the extracted text from Google books.
The extract below details the firing of torpedos and the blindness effect I mentioned in my question.
One scan and Van stiffened. Less than fifty emkay - out-system and 'behind' them - was the EDI track of something bearing down on the Fergus.
'I have conn!' Van triggered the emergency siren and diverted power from all the nonvital systems into the photon nets, the drives, and shields, immediately turning the Fergus into the oncoming ship - a heavy cruiser of some sort with distorted EDI tracks. Or an EDI of some type he'd never seen.
Torps inbound! came from Weapons.
Van caught four on the net monitors and put full power into the shield, letting the photon nets fade. Standard shields were supposed to hold against three, Not against four, and certainly not the old shields of the Fergus.
All the screens and detectors went blank.
Even so, Van could feel the wash of energy against the shipnet. As it subsided, he opened the detectors, shifted power to the nets, and continued to build acceleration toward the unknown cruiser.
Got them! There were two.
Van shifted power to the shields, but left enough for nets and screens to keep building speed and collecting hydrogen and dust - or before long he wouldn't have any mass for the fusactor at the rate of power he was using.
The main character is Commander Van C Albert of the Republic Space Force of Taran (RSFS). The cover blurb from the book on Goodreads provides the following additional information about the story. IIS is indeed Integrated Information Systems founded by the protagonist from the Parafaith War, Trystin Desoll.
Set in the same universe as The Parafaith War (but two centuries later, and intended to be read independently), The Ethos Factor is the story of Commander Van C. Albert of the Republic Space Force of Taran, a brave and resourceful officer who once defeated a larger enemy ship but indirectly caused the loss of a civilian liner in the process. Cleared by the board of inquiry, but an embarrassment to the high command, he retains his commission but is given only dead-end assignments. For a time, he must watch helplessly as cold war among economic, religious and political rivals evolves toward interstellar open warfare.
Assigned as a military attaché at the Taran embassy on Scandya, Van is seriously wounded foiling an assassination. Decorated, promoted and summarily retired while still in a coma, he wakes to find himself honorably but intolerably unemployed. Then the harmless sounding Integrated Information Systems foundation of the Eco-Tech Coalition recruits him to fly a starship, Van finds he now has a powerful new vantage point not just for observation, but for action. The IIS has interests everywhere and Van is not just a pilot, but their point man in a conflict that will shake the worlds.
Modesitt uses a distinctive blend of space battles, political and economic intrigue, and issues of race and religion to address deep questions of good and evil, ethics and self-interest. Van Albert makes his decisions; it is for you to decide if he is a hero.
The cover I remembered was this one: