I'm looking for what mods add new types of weapon (e.g. cannons, railguns, large rockets, orbital cannons, etc.) which should have nuclear versions, as well as any mods which add things like anti-matter, fusion, etc. which should be turned into T-N style detonations.

I've already got K2, SE, RFW, Bob's weapons on my radar, and I'll do a crawl through the mod portal later, I just don't want to miss anything obvious.

I'm also interested in nuclear-related mods, (like nuclear fuel, plutonium energy, etc.) for which I should change material choice, and any overhaul mods where material changes would fit (bobs, angels, etc.)...

Bonus points for suggesting any particular changes (e.g. rough yields of new weapons, costs of different weapons, etc.)

For Realistic Fusion changes suggestions, take the tsar bomb equivalent artillery shell and take the payload x10 and cost x4-8. Is it practical? No. Is it realistic? Factorio is set in the future, so yes.
Second mod is orbital cannons. I liked the orbital cannon mod that has SE compatibility, but launch enough and the auto firing was too slow. Add the equivalent of that but of course fixed auto firing and more powerful versions. Versions can scale with x5 cost and x2 explosion radius.
Haven't played SE yet. Would be cool if there was an interplanetary nuke perhaps related to the tsar bomb on steroids and smaller version for destroying moons. Cost maybe x1000 of the tsar bomb's older brother.

Edit: Would be cool if the bomb bigger than the tsar had a new recipe for it like matter/anti-matter stabilization and or/compression.

OK, I'll add them to the list...
I'll be doing a lot of re-working of RFW's support, and the yields of weapons will correspond to actual yields, but there is no reason why I couldn't add bigger antimatter weapons....

I also vote for Yuoki Industries suite compatibility, of course, if you have time or interest.

Oh, good suggestion, I've never really looked into it much, but I'll see what I can do.

I've looked into Yuoki a bit, and I can't really see any compatibility to add... Do you have any thoughts?

I'm still planning on adding specific support on my end for RFW, but that will be in a later release, as will MIRV.