Updating Server.app is not really necessary. OS X Mavericks clients are backward compatible with OS X Lion Server, in the same way Mavericks Server is backward compatible with Lion clients. It is only required to update Server.app if you want the new features available in the updated OS X Server, or if you wish to upgrade the host OS on the server (i.e. Lion Server.app is not compatible with OS X Mavericks).
Your list of active services mirrors mine on a server with only DNS running per the server app:
enabledServices = (
"com.apple.apspd",
"com.apple.collabd",
"com.apple.DeviceManagement.devicemgrd",
"com.apple.DeviceManagement.postgres",
"com.apple.DeviceManagement.SCEPHelper",
"com.apple.opendirectorybackup",
"com.apple.server.alertsd",
"com.apple.server.eventsd",
"com.apple.server.v2.stats",
"com.apple.ServerEventAgent",
"com.apple.servermgrd",
"com.apple.disks.smart.status",
"com.apple.xcscredd",
"com.apple.xcscredhandler",
"org.calendarserver.agent",
"org.calendarserver.relocate",
"org.isc.named"
);
In your case, the collabd should be running and it is complaining about the machine serial number. Check that your hardware serial number is in fact readable via software:
system_profiler SPHardwareDataType | grep 'Serial'
The best way to troubleshoot server when you don't trust the graphical server app (or want more details) is to use serveradmin command as opposed to the serverctl command. As you have noticed, serverctl is undocumented, so you'll want to stick with the stable serveradmin interface if at all possible.
Here's a short loop command that dumps just the running/stopped status of the various subsystems that serveradmin knows about:
for service in `sudo serveradmin list`
do
sudo serveradmin status $service | egrep "RUNNING|STOPPED"
done
You could easily change that grep command to stop only the running services...
sudo serveradmin status $service | grep "RUNNING" && sudo serveradmin stop $service
Best Answer
I found an entry in a thread on OpenLDAP.org's lists in which the commenter says that this is normal for BDB.
(Source: https://www.openldap.org/lists/openldap-bugs/201409/msg00057.html)
I have been chasing the same error for the better part of a week, and a lot of people report this error for many different versions of macOS/MacOS and Linux, so it seems... normal, maybe?
Hope that helps.
/Bill