I went to Goa at the end of September a couple of years ago and it rained solid for a week. Temporary shacks were closed & one permanent shack like the one down at St Anthonys in Baga was open.
I still had a great time though, it's a lot quieter, the countryside is beautiful, and was good to see another side of Goa that I hadn't seen previously.
You can find cheap hotels because it is not peak season, and parties are limited in September.
Although, I find Goa, a 365-day holiday place!!!