Got the fix that I wanted, and the solution I refused from the start.
Rename Saved Games\DCS to something else and it generates a new one that somehow fixed the previous problem, somehow.
UPDATE:
After several test and playing around with individual mods I've concluded that one of these mods that I used for template setup might be the culprit, removed three of them at the same time and my game back as normal, so unknown which one:
- SK60 [Not tested in detail]
- JAS39 [Confirmed by DragonOfTheArmory]
- Su-30 [Confirmed Cause] (thanks Nawi414)
- T45 [Probably/Most likely] (tested on server)
- VSN F-104 [Not tested in detail] (was removed in tandem with T45, unsure)
Some mods that me and friend tested safe so far:
- A-4E
- Hercules Anubis
- UH-60L
- OV-10 Bronco
- VSN YF-12 (Nawi414)
- VSN F-4
with symptomps of occurance based on my few testing as follow:
- JSOW directly hitting target
- Fused bombs not exploding and CBUs not dispensing
- APCs and Tanks (and probably more) placed in ME will not exist when said mission is entered
- Carriers gone
- LGBs ignoring laser designation
Test platform used: F14A/B, F15E, F18C, Client ME, Server
1Arc's post in Some Weapons are Not Fusing Correctly was marked as the answer