First, I don't believe a lot of the OpenNETCF.Net namespace is desktop compatible. There a re a *lot* of P/Invokes in there, and I'm certain that many are not wrapped for use on the desktop.
If you are using only a small subset that is working in both environments, great. However we have absolutely no control over what Microsoft may or may not do in future versions of their OS, so there's no way for us to know if the software will continue to work. Microsoft, at least on the CF and WinCE side of things, tries pretty hard to keep backward compatibility, at least over a few versions and especially for simple software APIs, so I wouldn't expect a change in the OS to alter the app. But again, we're not Microsoft, so we can't guarantee anything.