You should be able to silence the notification by deciding (with a rule) how to handle them.
When you allow any incoming connection for mDNSResponder permanently, you should never see this message again. If you do, please report the details to our support, reporting this as a bug.
If you want to allow local connections only, the "local network" factory rule of Little Snitch should already do that, unless you have disabled it. You can deny any incoming connection for mDNSResponder because the (more specific) factory rule for localnet has precedence. Again, if you still get notifications with an "any connection" rule, please report this as a bug.
And, finally, if you think that other IPv6 addresses should be included in the localnet-rule, please provide details. As far as I can tell, we DO interpret link local IPv6 addresses as localnet. But I'll forward the message from bugmenot to the responsible developer.