If you are refering to the valve that goes between the vacuum hose and the booster that would not produce the pedal to the floor that you experianced. The external valve only keeps vacuum in the canister. There is some valving inside the booster that must be malfunctioning.
As long as you have a vented gas cap, capping them should not be an issue, as well as leaving them un capped for the moment( other than insects and dirt and moisture and fuel vapors)
If you think you are pulling a vacuum in the tank leave the gas cap off while testing