I also suspect it's not an issue of the mod system per se. Why this fixed your problem is that "disabling mods" checkbox in fact disables Mechtek and stops loading the JSON files that cause this error. I highly suspect that its in fact `BetterBaseDefense` mod that changes some stuff in missions and produces the exception in a merged file. I have similiar issues with `JK_VariantsCAB` mod.
On a side note, if you remove a mod suspected of causing this, you also need to clean the Mechtek cache, for Heavy Metal (1.8.0-629R) it is in `C:\Users\me\Documents\My Games\BattleTech\mods\HBS` - remove `Cache` (and `Database` for variant related mishaps) folder and be prepared to see a different loading screen and a crash at next launch. Try launching again and the exception should be gone, and you will have a working BATTLETCH game with working mods again.