My super smart colleague managed to find the sensor template files. Made a copy of it, then edited it (since it was a simple XML file with definitions of states of different ststauses). In this case we simply adjusted the Not Initialized status of a warning state, to a green state. Then saved this custom sensor template to the customs area PRTG offers.
After restarting the PRTG services our custom sensor type could then be chosen for each disk sensor.
The only downside is since this is a per sensor thing there was no way to set this sensor template at the device. We had to change each disk sensor we had for each disk being monitored.
Obviously the best solution would be to have Synology have a way to initialize Hot spare disks, but I guess to them they don't want to send any I/O to the disk until it actually needs to be used. So this is the only work around we could come up with. Sorry for not having more specific details but I hope this helps others with the same problem.
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