I just include the map-bot-user-agents.conf in my base nginx.conf so it’s available to all of my virtual hosts.

When I want to enforce the bot blocking on one or more virtual host (some I want to leave open to bots, others I don’t), I just include a deny-disallowed.conf in the server block of those.

  # Deny disallowed user agents
  if ($ua_disallowed) { 
    return 444;
  }

server {
  server_name example.com;
   ...
  include conf.d/includes/deny-disallowed.conf;

  location / {
    ...
  }
}