It's worse than that. Because of the economic and legal disruption caused by effectively declaring software patents null and void, the SCOTUS may very well say,"Yes, we agree that this patent is not valid, but we've been doing things this way for a very long time, and it would be too harmful to our society to rule that it is not valid."

Bowman v. Government of the United States is usually the most cited example of this sort of finding (it deals with illegality of personal income tax due to Ohio not being admitted to the USA due to what amounts to a clerical error.)