Running a Legitimate Business in Wellstone City isn’t a half-bad idea. It gives characters a place to invest their money that is more secure than a bank; it gives them a steady stream of income in between jobs. Not only that, but if set up properly, especially if the PCs have two businesses or more, it can be a great way to launder money as well.
The business should be something that generates goodwill in the community. It is very easy to remove that good will if it is ever found out that the PCs are involved with the business it could turn the community against them. To ensure that that doesn’t happen, it is best if the PCs either use their legitimate names (if they are using aliases), use an alternate identity (if they have one) or are simply silent partners or angel investors. That way the reputation of the business isn’t tarnished even if the PCs are caught, framed, or worse.
It’s one thing to say that they are doing this, but doing it is quite another. Different GMs may handle this in different ways. Some might insist that there is a mechanical reason behind it, like your character (or characters) suddenly gets everything set up and then must take the Wealthy Edge in Savage Worlds or some up with another way to mechanically do this. Other GMs may just let it happen and let the characters reap the benefits of their hard work.
Of course, this makes the PCs vulnerable to the very sorts of things that they do. Insurance payments, hostages, robberies, people finding out that the PCs run the business and going after it to hurt them, and so on are all part of the risk of having a public exposure like that. The PCs need to be prepared for such things, and maybe they are so well known in the underworld that nothing like that would happen, maybe their connection is untraceable and the business isn’t at any more risk than a normal business of that kind. That lies in how well the PCs set it up in the first place.
One thing that it should not be used for is a tool to punish characters with. They’ve worked hard for their money, maybe they’ve saved some lives, maybe they’ve taken a few, but they shouldn’t be punished for using their money on something other than guns, bullet proof vests, and tactical gear. The city itself is punishment enough; let them enjoy their money until it’s an outstanding plot-point to use it against them, if you are so inclined.