After some more testing, I've reached some conclusions: Yes, it was an incompatibility with schall artillery. Here are the results:
Schall artillery + True nukes: ok
Schall Artillery + Mushroom Cloud: ok
Schall Artillery + Mushroom Cloud + True nukes: Error on startup
With Bob's warfare your atomic artillery shell (the one with 1 kiloton) gets overridden. The description stays the same, but everything else is changed.
Turns out your shells disappearing was because of a broken save, after testing in a brand new save it worked.
Not much of a problem, schall artillery becomes redundant with bob's warfare anyways, I just forgot to turn it off when starting my current bobs playthrough.
And one more thing, your atomic cannon shell (2 tons) aren't affected by mushroom cloud (meaning there are no graphical changes), is this intended?
My full modlist is: Total Automization - RTS rebalance, Aircraft (including aircraft realism and improved cargo planes), Cargo ships, FIll4Me, change map settings, dragon industries, geothermal, gun equipment, Logistic train network, mushroom cloud, schall ammo turrets, schall circuits group, schall tank platoon, schall gunpod, squeak through, unit control, warehousing, alien biomes, full Bob's suite (excluding enemies), microcontroler, spidertron extended, unlasting oil