Hi,
Glad to know that the issue has already been resolved and thanks for sharing the solution so that others experiencing the same thing can easily reference this! The reason I keep asking if you can see the synchronized users on the M365 portal is to determine if the issue is a sync to Azure AD or a sync to Exchange Online issue.
Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others", I'll repost your solution in case you'd like to "Accept" the answer : )
Issue Symptom:
In a hybrid deployment environment, when migrating users, the user list is found to be empty.
Resolution:
There is a custom rule in AAD connect which set msExchMailboxGuid to NULL for all synced users. After removing this rule everything works as it should.