Many ships leave from San Juan one-way through the Canal. We cruised the last week of October and only encountered a few showers during the 11 days. We disembarked in Acapulco. This was a great way to see many ports and experience the canal. The following week about 11/9, the return voyage encountered a Hurricane and had to alter its itnerary and disembarked passengers in Aruba. The storm just hung out over the Caribbean island including San Juan. You just never know. The Vision of the Seas was a perfect ship for sailing the canal.
September/October are a roll of the dice, since these are prime hurricane months for this part of the world. The water has had all summer to heat up and warm tropical water is the energy source for hurricanes. However, the odds are that you would not see one and you could well have smooth sailing for your entire trip. As others have advised, cruise captains make every effort to avoid really heavy weather.