I don't have an example of doing this immediately available, and I expect that this will involve parsing either a manually-created output channel or otherwise rummaging the DNS server logs.
If your firewall blocks all outbound DNS traffic except DNS queries originating on the server (this to avoid bypassing the DNS server, save via VPN or such), you can enable additional logging via the command line and then check the DNS server logs.
This configuration is probably more commonly implemented with either a network sniffer watching for DNS queries arriving at your server, or maybe a web proxy server, as that proxy server gets you the client information and the target host information, particularly given there'll be all sorts of not-web-related activity in the DNS logs for a typical client.
Apps network activity, app updates (various of which can appear to be HTTPS traffic, too), various data feeds, etc.
HTTPS and VPNs can throw a wrench into these eavesdropping and data-collection activities, unfortunately. They can either mask the access or hide the entire DNS query, depending on the computer(s) being monitored.
There are purpose-built approaches here including filtering (or logging) firewalls and OS X mechanisms such as Parental Controls, depending on the particular details of your requirements here. There are examples posted around the network of using Wireshark or tcpdump to acquire DNS data from your network, as well.
Details on managing BIND 9 from the command line — which is where this is headed — are available in the ISC BIND documentation, such as 9.10. Look for the logging statement grammar and setting up an output channel, as a starting point.
For the recent OS X Server releases, the BIND configuration files are located under /Library/Server. (See this discussion, as well.)
Modifications to the configuration files can sometimes derail Server.app, unfortunately. Shut down Server.app, make a copy of the file, incorporate the changes, then restart Server.app (and hopefully Server.app either doesn't tip over or revert your changes).