I know I am late to the party here, but I had a similar issue, and I think I may know what the problem is. The game seems to have an issue when multiple mods add the same thing. I had both your Naginata and Naginata Pack mods loaded (not realizing you (Siilk) made both, so I didn't notice the redundancy), and the game wouldn't load. But if I disable either one and just use the other, the game loads fine. I had the same issue when I tried to load Master Sword/Hylian shield mods made by two different people to compare them.
You are correct, this seems to be a problem game asset bundle loader is having for some reason. Modders have no control over that code unfortunately so the only thing we can do is to make sure item IDs are unique. So, of course, if two mods are adding the exact same weapon this issue is inevitable.
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