To ban players from your server by SteamID64 do the following:
If you are unsure how to find player's steamID64, check your server logs for the time when they joined.
1. Stop your server
2. Click Configuration Files
3. Click Config Editor next to Instance\SpaceEngineers-Dedicated.cfg
4. Scroll down to the ban section
5. Press "New Ban"
6. Enter Banned player's SteamID64
7. Save file in top left
8. Start your server!