According to JUSTICE LEAGUE OF AMERICA #0, Batman's reasons for his Tower of Babel files were "Fuck you, I'm Batman." He even thought Wonder Woman was just jealous she didn't think of it first. "Fuck you, I'm Batman." was also his reason for Brother Eye.
JLA Year One had J'Onn keeping those files because he was new to the "superhero" thing and new to interacting with humans on a regular basis. He'd been on Earth but had kept to himself for most of that time. Those files were also the reason J'Onn didn't want to vote Batman out of the JLA, because he felt it would be hypocritical.