Yup, plenty safe to do.
Regarding vm-pop3d.. in the services montior page, does it show it running or not?
Have you changed vm-pop3d to use xinetd/inetd instead?
DA checks for a process named "vm-pop3d" running on the system.. if it's being run through xinetd/inetd, then it won't show up (not executed until a connection comes in).
Another possibility is if the process name is "/usr/sbin/vm-pop3d" for some reason, which isn't matching "vm-pop3d" (check the boot script)
Either way, you can set:
vm-pop3d=OFF
in your /usr/local/directadmin/data/admin/services.status file to stop DA from going mad with it thinking it's not running.
John