Thanks for the report!
Unfortunately this is a known issue that I haven't managed to fix yet. Atomic bomb in magazines are also not working properly :/
For the bullets I think the direct damage works but the AOE doesn't, which is almost all of the damage gone.
(Mentioned in info page)
Atomic bombs do work in artillery shells and explosive rockets. But not really that useful in explosive rockets I guess...
All the capsule ammo is generated by code, I don't see why atomic boms don't work. I've inspected the generated prototypes and they look fine but still somehow don't work. I will take a look at another mods nuke mines and compare and see if I can spot any difference.
Sorry for the issues, thanks for trying my mod though :)
Hopefully they will work eventually...
I considered disabling those recipes so people didn't craft them and waste their atomic bombs and their time but forgot.