I'm doing the same as you, putting together several aircraft in a single DLC pack and I found this only difficulty. I thought it best to do this, leaving each weapons configuration separate and adding the corresponding line in the content.xml file. It works fine like that:

Well, someone could create a specific tool to merge vehicleweapons.meta, since it's kind of confusing like vehiclelayouts.meta.

Hello.

If some mod does not have tuning parts, is it safe to set a number 0 as an ID? Not only for a single mod, but also for several non-tuning mods. I want to know if these mods can have an ID number 0 to not occupy other numbers that would be needed for tuning mods in conflict with others.