The fall weather in Nova Scotia is a mixed bag (as with every season here). Last fall was unusually warm with temps into the 70's in october. However sepending on when you are cruising Sept or Oct there is quite a difference. Sept can have some nice warm days (called Indian Summer) that you would think it was July but the nights tend to cool off on those days so a sweter would be good. But generally late september and October you will want a sweater and light pants, however do make sure you have backup for a hot day. We tend to not get as much rain in the fall as compared with the spring. This being said, the meteorologists can't even predict our weather a day in advance so expect anything.
We were there last Fall on a cruise and will be there again this fall on another one. It was on the cool side and there was some rain. There is often a lot of rain on the Canadain east coast. Just go prepared aand you can still have a great time.