Lucius Fox explains that the chamber "can be flooded in case of a security breach," which sounds great, only that feature stops no one. First Bane steals the reactor, then when the "flooding" mechanism is activated later, it's so slow that even elderly businessman Lucius is able to get away from the room before getting even slightly damp.
"My shoes, your parents ... we've both suffered terrible losses."
Hilariously, when they're showing off the device and the security, Talia says, "Is Bruce Wayne really that paranoid?" That wouldn't have been our reaction. Keep in mind, it took about the same amount of effort to turn this reactor into a nuclear bomb as it would if it had just been an actual nuclear bomb from the start. Which is to say, very little. But where actual nuclear bombs are guarded by entire armies, this thing was sitting unattended in a basement in hopes that nobody would find the secret elevator button. There are people who keep their collectible Pokemon cards behind more security than that.
And why? Wayne wasn't using the reactor, so why keep it in a functional state at all? Why not just take the pieces apart and store them in different places? Hell, destroy the fucking thing and make sure to keep a copy of the schematics somewhere safe.
Perhaps encrypt them into the Bat-beard.