SQL Server 2000\2005 compatibility with Active Directory 2016
I have not gone through this process directly, but have worked with querying AD in a modern environment and a less modern environment.  I believe that the OLE DB Provider remains compatible between the older and newer versions of AD. Also I would not expect the loss of any commonly used (at least in my experience) properties, which would be the other risk.  

If you do run into trouble, however, I would be prepared to migrate the databases to a newer instance of SQL Server running those DBs at a lower db compatibility level.  This will still be challenging, as I think you can only go back to 100 (2008). However, from a mitigation standpoint I would suggest trying to go this route regardless.  This would also allow you to retire the older instances (and likely old servers they are running on).  Why not make a bigger project even bigger (though you can do it ahead of time, so it doesn't all fail at once).

I will qualify this with my of querying AD had been generally focused on getting basic user properties and group membership, and do it so infrequently I have to go look everything back up.  And it's been a few years since I have to do much Windows Admin work.