OK, ditched the problem of units causing problem with loading. It was simply impossible to keep tracking this stuff. It would take far too long and I have better things to do in life.
So I went with my another 'brainstormy' idea. Removed from GC map ALL fighters [*], transports (bulk and shuttles), and useless CR90s. Disabled also World Devastator's infuriating ability to destroy base defenses before battle even commences - added planet destruction ability instead and few light corvettes and Shadow-droids spawned from WD belly.
[*] - only one exception with few special Shadow-droid squadrons.
And you know what? It works like a charm. PR/OSH never worked so nicely. No lag, no hangs. Scenario loads in perhaps like 5 seconds. Wow! For now finishing Rebel-OSH campaign. So far, so great. Will test that with GFFA next.
As for adding Eclipse for Empire. Hmm it didn't worked too well. Ship is defenseless as it is basically only super-laser platform and it requires serious escort vs big fleet. Modded it with Sov and then Exec HPs to see if it'll behave as normal ship but no. It also didn't spawned fighter contingent I created. Real bummer... In the end added one Executor for it instead.
Anyway... to be honest I frankly didn't noticed ANY need for buildable fighters. I would support the motion to remove fighters (exception for few elite hero formations) from build menu entirely and permanently. Existing capital ship fighter complements are more than adequate to defend planet or attack enemy. Freeing so many units/research slots, oh well... just think of the possibilities for the future. Example:
Tier 1 shipyard: [troop]transports and fleet support ships (tenders, carriers, resupply)
Tier 2: frigates & corvettes
Tier 3: cruisers
Tier 4: heavy cruisers and battleships
Tier 5: dreadnoughts and super weapons