NEW YORK ( TheStreet) -- A judge's decision over a bonus brouhaha at Bank of America ( BAC - Get Report) is important because of the precedent it will set for other cases, and for shareholder lawsuits that may emerge as details are unveiled.

U.S. District Court Judge Jed Rakoff's request for more information about $3.6 billion in bonus payments for Merrill Lynch employees was shockingly basic in its scope. But related revelations could strike a blow to BofA's standing in court, as well as to other companies that reach regulatory settlements without "officially" admitting to doing anything wrong.

The Securities and Exchange Commission settled its beef with BofA last week, planning to accept $33 million from the bank to resolve charge that BofA made "materially false and misleading" statements to shareholders. The SEC claims that Bank of America had known about and approved the hearty bonuses ahead of the Merrill-BofA merger. It also says that information that was obscured from documents provided to shareholders before their vote the deal.

Shareholders have been railing about this issue for months, with at least one prominent investor spearheading a class-action lawsuit against BofA and a group of investors launching a campaign against CEO Ken Lewis, which ultimately stripped him of his chairman title. In other words, BofA's reputation has been tarnished for some time, and many have accused the firm of not being forthcoming about when and how the bonuses were approved.

The SEC settlement did little to actually settle the matter, since aggrieved parties will only feel satisfied once someone is cast as the villain, and forced to pay a price. BofA is not likely to do this easily, but Judge Rakoff isn't letting the bank off the hook with a fine that many observers have labeled chump change.

Though the judge questioned both parties at length, he ultimately asked the bank and the SEC to provide more information, most of which was fairly basic.

"I did not know much about the facts from the complaint, I did not know much, or really anything, about the basis of the settlement," Judge Rakoff said, according to Dow Jones Newswires.

Among the unanswered questions Rafoff raised were, How did the SEC come up with the fine, a figure that represents less than 1% of the bonuses distributed? What would have happened if the bonuses were not distributed -- would Merrill's losses have been $3.6 billion narrower? And who, exactly, is responsible for the decision to dole them out -- CEO Ken Lewis? Former Merrill CEO John Thain? Both? Neither?

"Was it some sort of ghost or a human being?" Rakoff asked.

That these questions haven't been directly addressed by BofA may seem puzzling, but it's not all that surprising. There's the obvious question of, If BofA was free of responsibility, why not provide evidence and avoid a fine entirely?

Maybe it will, or maybe it can't, but observers have drawn their own conclusions from the regulatory and legal meanderings. And if Bank of America has to challenge shareholder plaintiffs in court, or sit at a negotiating table with them, it would much prefer to have a less formal agreement with the SEC than a court-sanctioned admission of guilt.

Even more important, perhaps, are the implications for how corporate America goes about deal-making and how the SEC goes about regulating. Rochdale Securities analyst Richard Bove says the judge's actions mark a turning point.

"Historically," says Bove, "when company A wanted to buy company B, the discussions were not made public. Decisions on bonuses or any other range of activities were settled in private."

The SEC typically hammered out settlements with companies in private, just to let them know it was keeping an eye on the markets and participants' actions.

But post-financial-crisis business will not be business as usual, says Bove. Companies will have to be more transparent about details, and the SEC may not be able to "let companies slide by with miniscule fines for great misdeeds," he says.

Bove believes that BofA's actions were not illegal, and points out a sad irony -- that while these efforts are being made in the name of the shareholder, shareholders may ultimately be hurt by the government's heavy-handed moves.

It's true that this case may mean that BofA -- as well as competitors like JPMorgan Chase ( JPM - Get Report), Citigroup ( C - Get Report) and Wells Fargo ( WFC - Get Report), and others across the corporate spectrum -- may face an added level of inspection from the judicial sphere, tying their hands a bit tighter when jumping into meaningful business decisions. But shareholders were also hurt by lax supervision and the leadership that put Merrill under BofA's wing in the manner it did.

As a result, Bank of America now has an additional $20 billion of taxpayer support to pay down, as well as the intense public scrutiny that comes with it.

-- Written by Lauren Tara LaCapra in New York.