It is a pain to do now, and I do agree that we should be able to access all users through WHM's phpAdmin, as in the not so distant past. I manage all of the domains on my servers. We create special, limited privilege users only for mysql, used for script access. The WHM Database Mapping Tool is useless. But there are some workarounds to the PHPAdmin limitations that CP has placed on WHM.
If you are logged into WHM w/ root privileges, you can see the users for each table, and their privileges by clicking on the db, and then a table. You will now see the privileges tab within the table view navigation. You could use the information shown there to create an SQL Grant request, to edit a user's privileges (under the SQL tab). Of course this has to be looked at for each table in each database, because the privileges tab is not available in the table overview for the database. That's where the "pain" comes in. It only appears in the table view. There is also the "add user" link there. I haven't tried it in this scenario.