In that case I'm just going to assume that Shinra had no problem with people knowing that they were responsible for the bombing. It was deliberate and they didn't care who knew about it. In the case of Nibelheim though it was an experiment of theirs that got out of control, which would be disastrous for their image of being in control if anyone found out about it.
But yeah, that's just a guess
Well first, Banora looked much smaller even than Nibelheim. Secondly, what exactly are theorizing that Shinra wanted to cover up? That their hero went on a murderous rampage or incriminating documents? Because the documents survived and were only destroyed later. And no hero flipped shit in Banora.
Banora was definitely more of a big deal than Nibelhiem, being the only known exporters of the Banora Apples, and a juice that Genesis made that won the National Banora contest of sorts.
SPOILER ALERT!
But yeah Banora definitely needs to get analyzed.
edit: See THAT makes sense. ^ I forgot that one took place before the other.. but what info can be leaked?! WHAT?!