I always assumed the fire rate upgrade applied to all weapons, although I had the impression drones just did their own thing (and I hardly used Thor).
Now it turns out that both mortars and SAMs are not affected at all by this upgrade!
For SAMs it's pretty hard to test, as you can only time the delay between the first and second missile, but mortars should fire once per 2.5 seconds with the upgrade instead of once per 2.92 seconds.
Note to Virgil: I'm not busy bug hunting or something like that. I'm just running into these things while making quiz questions and designing some special maps. I am very surprised myself I only found out after almost a year of playing, just like the 0.1 emitter interval bug. Needless to say I still like CW a lot! :)
To speed up the SAM fire-rate (kinda) is to use speed nodes to get packets there faster. At least thats what I see and think.