In many ways, Japanese organized crime is no different from other organized crime groups. As described in Peter Hill's research, organized crime's basic business is protection. The yakuza is no different. Just like the mafia, they protect their own ability to do business effectively, and also they have to protect their own customers or someone would move in and take over for them.
What's been different about the yakuza for so long isn't what they do, or even how they do it, but how people see them and how they present themselves.
For many years, the yakuza have had sort of a truce with Japanese society. For years they stuck to mostly "victimless" crimes and were left alone. Things like gambling and sokaiya (shareholder meeting disruption) were either not considered to directly impact the general public or in some cases were actually legal.
Police would, of course, make a show of hassling them. Police raids on gambling operations, interrogations, that sort of thing. Except that detectives would warn the group about the raids so they could clean up the important stuff and set out some nice souvenirs for the officers to take as proof of the raid. They'd usually warn them when they, you know, stopped by for tea.
The yakuza haven't been without their benefits, either. As protectors, they have to protect. That means stopping random crime on their turf; punk kids, bosozoku gangs, drugs and whatever else wasn't under their jurisdiction. For a long time, many yakuza stayed out of drug running as well, considering it below them.
Because of this public tolerance, yakuza have been able to do things the American mafia never could. For example, a family might have an office with their crest above the door. "Headquarters of Tojo-kai," or something like that. Yakuza would come and go during the day, maybe stand and smoke outside. And you could tell a yakuza on-sight because they dress and walk differently than other people in Japanese society. In David Kaplan's Yakuza, a customs officer relates from his work that it's easy to tell a yakuza stepping off the plane from Japan versus other passengers. The fingers, pompadours and punch perms are one thing, but the real identifier, he said, was the walk. Yakuza strut. They walk with a swagger not usually seen in Japanese mannerism.
Aside from having offices and being quite obvious in mannerism, yakuza also carry business cards. Ryuji Goda, Omi-rengo. Sometimes they'd be left at a new restaurant so the owner would know where the protection money goes, or as an subtle notification that yakuza are involved in whatever dispute.
Speaking of disputes. Another way yakuza are part of daily society in Japan is that Japanese citizens see them as a viable business solution. When a dispute comes up that would involve painfully lengthy negotiation, the citizens- maybe small business owners, or someone who'd been in a crash trying to get money from their insurance company.
But times are changing. As the characters in Beat Takeshi's Outrage are killed off one after another, one remarks that the days of the traditional yakuza are over.
The yakuza encroach more and more on daily life. They hassle innocent people, engage in human trafficking, or even murder. Police have been forced to crackdown as public tolerance for the criminal element recedes, leaving them more exposed. Businesses have been more-or-less forced to put up signs that say they won't associate with yakuza in any way. The National Police Agency in Japan has put out a quota of 20 yakuza arrests minimum per month in per prefecture, according to an article from Jake Adelstein on JapanSubculture. Those warnings that preceded raids have stopped almost completely, the article states.
So are the yakuza going to fade away? No, of course not. They're just going to resemble the American mafia that much more. Publicly visible offices will be replaced with more subtle bases. Business cards won't be left lying around. Things will continue to move underground. The yakuza aren't going anywhere, no matter what society says, and if anyone can adapt to change, it's them.