But that's the point, as long as they KNOW he has them he's their instant target should some homcidal being take control of them and access their memories. "Nuzzink in ze vorld can stop me now... oh wait, zat bat guy in Gotham, he could... zo let ooz zee how far zis heat vision can reach"
As long as they DON'T know he has them, he's less of a target at a time when he needs to NOT be a target so he can implement them.
Again, I keep remembering a line of fanfic that came out after this, when Dick calls Clark on their decision and Clark replies "You think he has a file on how to stop you?".
Dick's reply is "I really hope he does, because if something were to take control of me and use the skills I've learned to hurt or kill innocent people, I'd WANT there to be someone who would know how to stop me, and Bruce is the one I'd trust to do it. It would be the hardest thing he'd ever had to do, and it would probably destroy him, but he'd know it's what I would want."