I'm not a VMware employee, so take this for what it's worth. I believe that disclaimer regarding the deprecation relates to the fact that all new VMware user interfaces are being developed using FLEX. And there is a rough plan to port the vSphere client from .NET based (current) to FLEX based, but all estimates that I have received indicate that this will not happen for 2 years. So if you want your plug-in to function anytime in the next 1-2 years then you'll need to develop for .NET. Obviously, if there is anyone listening who has intimate knowledge of this plan, I'd be interested to hear it. Thanks.
You are right. The pdf in the next post from VMware Technology Exchange session mentions it.