Has anyone experience with the inplace upgrade for the OS from 2012R2 to 2016 on the scom management Servers and the database servers? What are the steps to take?
I would agree with Jasper. Bring up new server add them to the pool migrate everything over and then retire the old servers. One thing to make sure of though is that you Migrate the RMS Emulator role. Also moving SQL there are Reg keys and config files that need to be updated and if you do not do this correctly you will have problems do a bing search for moving scom database there is documentation on it.
Personally I would recommend against it. If there is not too much third party software on the management servers I would recommend to deploy new management servers in the resource pool and migrate everything there.
I would also take the same route for the SQL instance, simply move the databases to a new instance.
This will most likely take less effort and downtime than upgrading the OS. In general I would always recommend against upgrading a Windows Server OS.