Wp-admin Custom User Management

Always use the existing functions, if those functions do what you need. That way, your code has the best chance of staying functional as the Core changes. If you make direct queries to the database then you have to keep track of changes to the database and alter your code accordingly.

Using Core functions also means that hooks have the best chance of working where they are intended to work. If you make direct queries to the database you bypass those hooks, unless you make a special effort to support them. Again, you will have to monitor changes and update your code accordingly.

Also, the database is complicated making some queries are extremely complicated and easy to get wrong. Let the Core handle it when it can.

I am not against making direct queries the database but it is not something that should be done lightly. If this is a first plugin, avoid it if all possible.