An outer hull with enough water to shield against flare weather would be extremely heavy. You'd never get that many tons of water into such a thing without flying it to Saturn and processing the ice in the rings. The "storm cellar" needs to be inside a tank somewhere inside the ship, with enough emergency quarters and supplies to last out the storm. There is also the possibility of using electromagnet shielding of some kind. The storms consist of charged particles. I don't know anything about shaped magnetic fields but one large permanent magnet might be the way to go, with some kind of extenders to lead the magnetic field to the outside of the ship to trap or divert ions. Then there might be targets at the poles that will entrap anything that makes it there, using a lot less material Paraffin wax might be good.
Answering a concern a bit earlier in this topic, rip-stop fabrics can back up vacuum-proof fabrics. I'm sure that the fabric is already available off the shelf, too.
Oh, and if it has to be that way, the storm shelters might be electromagnetically shielded. I would prefer permanent magnets if at all possible because permanent magnets still work if the power is off.