I've updated my QNAP to QTS 4.2.0 and guess what ... all my Apache Virtual Hosts have disappeared ... wonderful ...
After a lot of searching, the solution was simple: QNAP, in their infinite wisdom, disables ALL Virtual Hosts after the upgrade.
To enable them again:
Go to your QNAP webinterface, open "Control Panel" -> "Applications" -> "Webserver" and click the tab "Virtual Host".
If you're in luck, then you'll see you old virtual hosts still listed, but disabled.
Check "Enable Virtual Host", check all the virtual hosts you want enabled again, and click "Apply All", and your virtual hosts will be online again.
For those unfamiliar with Virtual Hosts, the simple explanation:
You can define a directory on your webserver, which should be seen as a "separate" website.
You can call this virtual website, either by a specific name (your DNS or the /etc/hosts file on your computer needs to map this name to the IP address of your QNAP), or specific IP port.
This way, it looks like more than one webserver is running, ...