I am not from Soti and my answer is by no means official.

MobiControl device agent version is getting more and more de-coupled from MobiControl server version in recent years. For Android-Enterprise device platform,  the device agent to be used should, in general, be chosen based on compatibility with the device firmware version and/or on the use of any new features offered by newer device agent, rather han based on the MobiControl server version.    Most of the basic features should be compatible across different device agent versions, though it is possible that something might occasically break.  So, to be 100% sure, actual tests at least for critical features used on production devices should be done BEFORE performing upgrade on either the device agent and the MobiControl server.     

Thanks for your answer.

Can you tell anything about Windows CE / WM devices?
I can generate a new client after upgrading the server.

Can I somehow get new agent before upgrading? (or do I need to retreive this from another server)

I've played with a small number of Windows CE/Mobile devices, but haven't touched any in the last two years or so.   As the device agent binary of such devices  are generated from the MobiControl server, enrollment of such devices should be quite straightforward.  However,  whether existing enrolled devices will remain in full control or whether the new device agent binary should be installed before or after the MobiControl server upgrade is likely to be more complicated and might different with firmware version and device brand/model.   Even if you get answers from Soti experts, I believe it is still much safer to try out the suggested flow on a UAT platform before proceeding with larger number of production devices.