I think the only sane answer would be a clearcut Yes, but the question is also highly misleading by insinuating that software patents actually cover innovative theorems. The vast majority of them don't.

Austin Meyer, the maker of the X-Plane flight simulator, was sued for millions of dollars because his app used an in-app purchase option made available by an existing 3rd part SDK.

There is a whole industry of inventing bogus software patents that take utterly trivial everyday business processes like giving someone money for a product, dress them up in fancy lawyer talk and general descriptions of non-existent, "systems" or "methods" without any example or prototype, and then sue people over it. In-app purchases? Better pay up! You have a fax machine or scanner? Pay! Storing business data on some electronic device for later retrieval? Better pay an arbitrarily high patent license fee!

It's absurd.