It's difficult to keep unfair arrangements when all is transparent. You can't just implement transparent salaries, without also making the salary scale fair. And the benefit there is that once salaries are transparent, everyone knows that they're fair, because they can verify it for themselves.
If you can't fix discrepancies in an acceptable amount of time then full transparency forces something unpleasant, and in this context it is potentially unhelpful to everyone.
A good example of transparency not helping is our sudden transparency about the activities of the NSA. Obviously that's not helping them. Though arguably it is helping us.
In a case where a company is intrinsically unfair to its employees and can't correct that, transparency would probably hurt the company but help all the employees - by sending a strong message that it's time to get the hell out of this crappy company.