It's also much more complicated to define "silent" in the context of a virus. In a larger-genomed organism there is a relatively clear (though still not completely clear) function of a coding region, where the change of a nucleic acid will have no effect on the protein made - but still might (subtly) effect regulation in some way.

In a virus, most nucleic acids have multiple, layered, and unknown functions - it's much much harder to assign any given nucleic acid as "silent", and be confident that that is the case from an evolutionary perspective.

As another posted, it's a good hypothesis that's straightforward to test statistically against all of the other variants. But on its own, it's not necessarily convincing here that the S/NS ratio is particularly concerning (and as above, doesn't speak to how directed evolution works either).