Assuming there is a Linux professional helping to get everything working for the business owner, this may not be an insurmountable problem. On the other hand, if the switch to Linux is being accomplished by a non-tech savvy business owner, it may lead to some tough platform choices for those involved.
Most of the time one can deal with these problems by leaving one existing workstation installed with Windows, to handle legacy peripheral problems such as this. This solution is also helpful for future peripheral purchases whose compatibility is not yet known.
As stated previously, though, thanks to CUPS and SANE, these cases are far and few between. It's only a problem with select "made for the enterprise world" type devices such as business card scanners, etc.
Is making the switch really worth it?
The bottom line isn't always as simple as dollars and cents. Sometimes, it comes down to individuals deciding whether or not switching over to Linux is really worth it, despite any perceived benefits of cost cutting.
My opinion on the matter is this: With a professional helping with the migration, moving most of a small business over to Linux workstations/local servers and other devices is not out of the question at all. The key component is finding a skilled individual to facilitate the migration effort. This, not the software or peripherals, will dictate whether a given Linux migration will fail or succeed.
As to the perceived "value" of any Linux migration for a small business, it comes down to priorities for those involved. If a small business is content with relying on proprietary software for their day-to-day needs, realizing that in many cases a missing license key means more money to be spent down the line, more power to them.
If, however, that same small business decides they're tired of spending money on software that could be replaced by open source alternatives running on an open source operating system like Linux, then investing in a platform switch clearly is the way to go.
I believe that the key to successfully appealing to small business owners and getting them to see the benefits in making the platform switch comes down to one very important thing: value to the business.
How this is done really depends on who handles the migration for the business owner. But if a clear, outlined value can be demonstrated without ignoring possible challenges in making a switch to Linux, then no question remains that migrating more small businesses to open source freedom is completely doable.