From my experience in the last few years, having always been land based, the weather in september - october is very unpredictible.
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September 2010: South Ari atoll, Rangali island: 3 weeks of rain, almost non-stop, a lots of trips were cancelled, due to heavy wind, and the all island was a lake, our clothes were getting all moldy, as well as our rooms, and of course, all the guests were very happy and smiley ^_^
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October/ November 2011 even the beginning of December: North Ari atoll, Halaveli island: very vary and some heavy rain, we had to cancel a few trips, but we were more protected on the inside of the atoll, so we could still go out to some protected dive sites.
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October 2012: Laamu atoll, Gan island: a lots of wind and rain, we couldn't take the boat out. November was impredictible too, but we had some good days of diving.
The rain doesn't affect much the dive in itself, it's just going to be a bit cold on the boat. Except when the rain is just that heavy that you can not see where you are going, neither the shallow reefs to avoid :-S and, if it happens during the dive, the boat crew can not see where the divers are coming up. It usually doesn't last long, however, when there is no wind, it can be on for a while.
The wind is really affecting us, even when it doesn't rain.
When it's too rough, it's too rough. When even the boat captain is saying it's not good, and all the fishing boats are back, it's best to not give it a try.
As said xabain2003, it can be difficult for us to plan the dives at that time of year, as some dive sites might not be accessible.
With a liveaboard, I believe it's easier to avoid the bad weather, however, sometimes it's all over the place
Hope you will get lucky (over and underwater) and wish you a wonderful stay in the Maldives!