>It is only used in the `program-arity function`, which is not called anywhere in the Guile repository (and calling it with valid inputs results in an error due to the `program-arities` being undefined).

This is untrue, it (i.e. program-arities) is also used in the manual.

>Removing those functions is simple, but the `arity:` accessors have more users, […]

It shouldn’t be removed, rather a replacement should be provided somewhere.
Regardless of the changes to the VM, compiled procedures still exist, and by definition that’s what a ‘program’ is, so ‘programs’ still exist, and hence many of the procedures in that module still make sense, including  program-arities. In particular, arity information is still recorded (in .guile.arities), so it should be made / kept accessible somewhere.

Best regards,
Maxime Devos