Ok, I thought about VMware for some reason
In Hyper-V it's a little bit different, so to make this VM not being counted as being in down state when it's powered-off, you need to disable the monitor for Power State - in this case only the other 2 monitors (health and heartbeat) will rollup to uptime. So VM will be in a down state only when it's powered-up and having issues reporting heartbeat or when hyper-v server reports its state as unhealthy.
Again, you can create a group of VMs and set such a disabling override for the group and then add VMs to the group manually or by a certain rule.
If you still need to exclude such VMs from the Uptime report, you will need to create such a group, which is not something you can do in SCOM out of the box, but there are some instructions on how to do that:https://sentryboy.wordpress.com/2008/06/30/groupcalc/