The part I don't understand, in terms of infringement, is that profiles are not product for product equivalents to the amp they are profiling.
A profile includes a whole host of things, including amp settings, guitar pedals, speakers, cabinet design, mics, mic pres, console settings, talent, etc. If an amp manufacturer has a valid infringement case, then so does every manufacturer in the signal chain. Can Shure sue Kemper for infringement for reproducing the sound of an SM-57 mic'ing a guitar cabinet? AKG? Or what about Ruper Neve? Or Celestion?
I would liken it to Sherwin Williams (paint manufacturer) suing Home Depot for taking another brand of base paint to create a custom color match for a customer.
I imagine a manufacturer could be enough of a thorn in the side of a profiler to make them capitulate, but I bet they'd lose in an actual court case.