> That doesn't answer the GP question:

It does.

They asked

   >>> Does Signal protect from the scheme when the government sends discovery requests for all existing phone numbers (< 1B) and gets a full mapping between user id and phone number?

Which yes, this does protect that. There is no mapping between a user id and phone number. Go look at the reports. They only show that the phone number has a registered account but they do not show what the user id is. Signal doesn't have that information to give.

  > Can they connect a number to a username?

From Signal

  Usernames in Signal are protected using a custom Ristretto 25519 hashing algorithm and zero-knowledge proofs. Signal can’t easily see or produce the username if given the phone number of a Signal account. Note that if provided with the plaintext of a username known to be in use, Signal can connect that username to the Signal account that the username is currently associated with. However, once a username has been changed or deleted, it can no longer be associated with a Signal account. 

This is in the details on[0] right above the section "Set it, share it, change it"

So Signal cannot use phone numbers to identify usernames BUT Signal can use usernames to identify phone numbers IF AND ONLY IF that username is in active use. (Note that the usernames is not the Signal ID)

If you are worried about this issue I'd either disable usernames or continually rotate them. If the username is not connected with your account at the time the request is being made then no connection can be made by Signal. So this is pretty easy to thwart, though I wish Signal included a way to automate this (perhaps Molly has a way or someone can add it?) Either rotating after every use or on a timer would almost guarantee that this happens given that it takes time to get a search warrant and time for Signal to process them. You can see from the BigBrother link that Signal is not very quick to respond...

[0] https://signal.org/blog/phone-number-privacy-usernames/