Yes, the app that runs under RhoElements 1 will work without modifications using the runtime from RhoMobile Suite.
To build native application you need Visual Studio and required sdks.
but I am not sure about the support of winCE in VS2010.
I think the workaround will be building application using RhoHub, but have not tried with 18.104.22.168 build.
VS2010 does not support building for Windows CE.
As Patro says, you can use the runtime from RhoMobile Suite for the smoothest upgrade experience. That would be my recommendation based on your question.
If you particularly want to transition into a native application with MVC then check out Geoff's slides from the 2012 America's app forum: https://launchpad.motorolasolutions.com/appforum/presentations/rhomobile/appforum.chicago.pdf