To me, it's not so much about failure to report as it is about separate entities that make the owners money that is not under the team's finances.
The NESN- Fenway Group is a good example. While the Sox are not the only thing NESN broadcasts, it's clearly their number one money maker, and it is essentially owned by the group that owns the Sox, The money they make off NESN does not and really should not count as Red Sox revenue or profits, but it is a way the Sox owners make money off the Sox without it being counted as revenue.
I'm not sure if the Sox also have a separate concessions and merchandizing company handling that aspect of revenue generated by the team, but I think several teams do. That money would not be on any revenue ledger of teams that make it its own company.
These are the types of examples I'm talking about, but I also would not be surprised if owners do some book cooking, as well. That, however, was not what I meant by "hidden revenue and profits." (And "hidden" is not really a good word choice, since much is out in the open, but it's just not counted at MLB revenue by teams, or am I wrong?