I am very new to SH5 modding scene and have no idea how extensively can you mod it, but I have a feeling that it's not possible to change the sub itself because someone would have already done it!
Can someone comment on this?
Would be cool to have different mods to transform the sub to different subs, though.
Having nuclear missile capability on the other hand is completely new mechanics so, unless you can really code in addons such as new "stations" (like the map, hydrophone, radar etc.) and from what I've seen so far, it's not possible.
interesting question tho and welcome to the forum!