Assuming what you say is true about the software, sales tax returns still have to be filed. And while automated filing is likely less burdensome as compared to the old ways, it's not cost free. For smaller companies, this could lead to large increases in accounting expenses incurred.
There could be other costs incurred, like having to work with state revenue auditors that might want a peek. And not just from one state either.
The cost structures for businesses are often quite different between smaller companies verses larger. The larger companies usually have the administrative ability to absorb additional tasks without adding to their administrative overhead, smaller businesses not so much.