I think they are referring to the non-litigation clause in the Opus license. Oracle probably charges extra for taking on the burden of potentially not litigating because of that license.
We asked some folks at Oracle about this, and my understanding is that this fee is imposed by the vendor providing the Opus implementation for their DSPs. Oracle is just passing on this cost. A specific implementation may, of course, include technology which has additional licensing or fee structures on top of the basic royalty-free license used with the reference implementation.
I doubt it, Digium is scared of patents but the SFLC seriously considered going to court to get the known patent declarations declared invalid. If someone had gone after Digium, I'm sure the SFLC would love to hear about it.