I have never seen any differences between players that lead me to the conclusion that some of them were affected by rain and others were not, nor have I ever seen anyone suggest this until you. As far as I know the server checks the weather when the map loads, and applies the penalties for that weather for the entire duration of the map. Which means that if the dynamic weather system switches weather during the map, people joining will get the new weather client side, but the server will retain the weather penalties it loaded at the start of the map.
Differences in visual weather for people playing at the same time, yes. Differences in mechanical weather, no. Of course that still means that differences in fog could give players with lighter or no fog an advantage in visibility.