Password protecting your jumpgate would only be useful if the attacking force couldn't generate a jump point without gates. Since most large military vessels (of the major races, don't know about the minors ones) can enter and exit hyperspace with the use of gates, the use of password protecting the gate would be questionable.
As a minor point, and using the case of B5 especally, if they had to evacuate in a hurry, you'ld have to give the password to each civilian vessel, which would slow thing down. Because someone could leak the 'password', you would not be able to give it out until the evaculation began.