Hi,
VM still responds to ping requests.
I will assume that the VM is still running.
But cannot access VM via SSH, Apache non responsive, and SNMP monitoring reports server down.
As first step, I would monitor what happens in the VM level. Monitor the vents of changing firewall, stopping of Apache and all you find as not available.
In first glance following the information provided it seems like an internal issue and not host level issue (but with the information we have it's more guessing than conclusion or assumption)
In the Azure portal the Agent Status changes to ‘Not Ready’.
This says not a lot since it is possible be a result of what's you have internal which close the the services
100% repeatable.
It might sound confusing but this is a very good information for you. A consistent behaviour which you can reproduce means that you can monitor and examine and you (or another experts) should be able to find the solution in most cases.
next step is monitoring....