Microsoft Graph API : Some attributes are null when filtering by signInActivity/lastSignInDateTime

Are you getting the data for the same users though? Keep in mind that when you query the signInActivity property, Graph makes a call to a different service on the backend, and only then correlates the results with the user store. There are few implications here, the first one being that said service doesn't give you real-time data, so any changes in user properties are not reflected immediately. Another one is that the service returns sign in activity for cross-tenant access, that is it gives a separate entry for when a email address removed for privacy reasons accesses any other tenant, and said entries are populated without any user details apart from id. I wrote an article about this a while back: https://www.michev.info/blog/post/5845/non-existent-users-show-up-in-sign-in-activity-data-or-how-logs-continue-to-disappoint 

So now that we know permissions are not the issue, make sure the user data is in order. The article above also tells you how to query the AAD reporting service directly, so you can see the "raw" replies therein.