Those ships that were struck by a spinal meson or two are going to be questionable. A Zho dreadnought's Q mount on average logs about 4 1/2 jump drive hits, 3 1/2 power plant hits, trashes the fuel tank 85% of the time, delivers a bit under 9 hits to screens and 3 to computers. If the Imperial fleet was forced to withdraw (as happened a lot in the early phase), the 85% with the shattered tanks were unable to retreat with the fleet or retreat to the outer system; they were scuttled or captured. Those that could be repaired by the Zho either made their way to Zho space where they could be studied or got repaired and joined the Zho fleet only to get shot at by the Imperials when they returned for round 2. And if they couldn't be repaired, I'd have salvaged whatever I could and then steered them into the local sun to keep them from being recovered by the Imperials.
Even the Zho cruiser H-mount will trash fuel tanks on a successful hit 2/3 of the time. In a duel of ships of the line, it really comes down to whether or not you took a hit from a spinal meson and whether your side won. If your side lost and withdrew, your cripples are mostly lost.
And, according to TCS (AFAIK the only supplemet talking about such repairs), how will it take to repair it?
Regardless how many damaged systems a ship has, it can be repaired in a small fraction of the time taken to build one anew, and even those crippled by a critical (unless vaporized, off course) can be repaired in a few weeks for a small perecentage of what is needed to build it.
So, you're right most of the losses will come from scuttling the crippled ships when you have to retreat, but if you hold the "battlefield", most your losses could be repaired with time (and 5-6 years are quite some time for that), and even if you retreat, unless it is a rout, I guess some of them might be recovered by tenders and taken to the rearguard for latter salvage/repair.
Off course, as told in many other threads, I see it as one of the main flaws of HG when used as campaign, as most traveller background (best example is Rebellion), talks about huge shipping losses that cannot be recovered, while if using HG/MT rules (and most of it in the Rebellion, where ships are similar, if not identical, in both sides, and so easier to repair/salvage) most this lost shipping will be recovered soon just with repairs (new builds aside).
Indeed, even if ships don't sink in space, constructive total losses will be quite frequent in HG2. Nonetheless, the issue remains, whatever the answer. As long as some ships are salvagables you will have to ponder the issue of "should I use this yard to repair or built?"
While new building can be standard product, hull repairs are custom jobs requiring specialised personnel. No "trained monkey job". Systems and sub systems can be "repaired" by assembly or sub assembly substitution (with diagnostic ...etc), but the workers used are a solid notch abose the assembly line workers that produced the assemblies as components. Its the best yards that will have to be used for repairs.
Or put it another way, even if you can figure building capability of the sector, some of the best of your yards capability will not be available for building unless you give up repairs.
Once again we must remember SM is a critical hot frontier for the 3I. As you say, most shipyards busy with repairs won't be able to build new shipping, but those new hulls may be built elsewhere in the Imperium, while local shipyards being dedicated to repairs, as the same hull that hight be worth repaireing might not be so worth taking far to repair.