1. If you have a VM, what options do you then have? Hardware health is obviously not an option for a VM. Is that where vCenter and ESXi host monitoring comes in?
Hardware Health information is available in SAM for the ESX/ESXi or Hyper-V hosts no differently than it is for Windows or Linux hosts.
2. If SAM for a reason cant read the hardware health due to compatability issues. what options do you have here?
If you have another vendors hardware that is not supported by SAM you can use SNMP Monitors or NPM's Universal Device Poller to monitor hardware health on those systems
3. For a virtual machine, if the disk that Windows see have issues or disappear, how can admins be alerted?
If a monitored volume disappears from a Windows host it will go into an "Unknown" state, which you can alert upon if you wish.