Do all the apps that work in Gnome shell also work in Unity? Or if there is a limitation is there some way to know that without actually trying the app?
They work mostly. You could check the package in questions bug tracker to see if anyone has had issues yet. If not, try it. If it doesn't work report the bug to the package.
In my opinion Ubuntu is free. Part of what you morally pay for it is trying packages and trying to sort out bugs/report bugs.