I think everything concerning a protocol should be in the same module. C.f. Protocols.pmod/HTTP.pmod/module.pmod that (among other things) contains a bunch of utility functions. Those functions don't implement the http protocol, still I don't think they belong in Standards.HTTP. That'd just be confusing.
In the case of IPv6 it's unlikely that protocol will ever be implemented as its own Pike module. Even so I think the same argument applies - it's a protocol and hence I expect to find IPv6-related stuff in Protocols.IPv6, just as I expect to find http-related stuff in Protocols.HTTP.