O.k... First of all my apologies for mispelling your name, Requiem_for_a_starfury.
Now, down to business:
1): as far as I know the only objects which have two sets of sequences are items like flares, explosives and so on. They are hardcoded, period. You can simply turn the rain self visibility on and off (better then constantly spawning and destroying, now that I think about it).
2): I think that rain damage must be dealt via script in any case, just like critters poisoning the PC. As far as I know radiation poisoning is always dealt this way in both Fo and Fo2.
3): You can have both short and long storms. As I said it's a simple piece of code in a script.
See you.