There are two schools of thought on lay-up storage.
The more popular is to have the tank as full as you can, with a fuel stabilizer added (we call it Sta-Bil here in the States).
Or you can do what I do, which is to drain all the gas at the end of the season, and remove the petcock so you can inspect for any water or crud, which could include the original factory lining. I then leave the fill cap off for a few days to allow the tank to dry completely.
The water you found could have come from condensation. Was it in the left carb? Do you park the bike on it's sidestand for long periods? (overnight?)
Also, be sure to remove and dump the gas that is in the bowls at the end of the season.