Are there any US court cases that suggested treating encryption as something covered by the Second Amendment? It would be more strange than putting malware under the Second Amendment. I can appreciate the gotcha of "if the US government defines encryption as arms then the second amendment applies" to disincentivize such a definition, but the government could simply call encryption something other than "arms" and thus avoid the Second Amendment.

I think the general consensus in the US is that encryption falls firmly under the First Amendment. It's not as if the First and Second Amendments are necessarily mutually exclusive with respect to any given tool, but I think case law is such that the Second Amendment doesn't apply to encryption.