I am currently considering my options. (congrats for finding the railgun recursion issue)
My problem is that as far as I am aware I can't check to see if someone has setup there railgun recursively.
I have thought of a number of options none of them good.
Option 1 remove the junction which probably would be a balance plus but I enjoy having multiple emitters on one rail.
Option 2 make it harder to exploit by filtering the parts that can hookup to a junction note that this makes things more difficult from a usability standpoint and doesn't fix the underlying problem.
Option 3 I "may" be able to cap the damage but that only induces many smaller rails and punishes anyone who hits cap with out using the exploit.
So if someone can find a better implemental option I would be delighted but currently I am going to log it as a "if you want to abuse the rules and win go for it"
As for the Nukes It is now under consideration.