Hi John,
Thanks for the request. At this time there are no custom CSS settings within SmarterMail 16.x. (Though I believe this could make a come back when themes are introduced.) That said, you can still apply custom CSS to your installation by modifying the system files. Our article, Skinning SmarterTools Products, explains more:
This process can be used in the meantime, and I'll forward your request to bring back the custom CSS section.
Thank you,