I agree that it's entirely in what you need to do. If you are writing some routine to automate or abstract list management, then the Web Services may be easier to leverage (and your code will be more portable) and performance wouldn't be an issue.
However, if the stuff will always live on the server, then there's no problem using the API.
One thing the Web Services will give you over the API is AJAX-style dynamic client abilities.
What are you trying to do?