The .NET version users have on their machines makes is immaterial. In fact whether they have .NET on their machine or not is immaterial. Any .NET code in your site is run server side not client side.
Internet Explorer reports the version of .NET installed in its user agent string. If Google Analytics shows you the user agent strings for the browsers used to connect to your server, you should be able to verify the version of .NET.
Some browsers allow users to change the user agent string used when connecting to web sites; you could think a user has installed .NET when it's not true.
I am not sure what the importance of knowing that is, though.
At this time, you can't get at the actual user agent string data with Google Analytics, and GA does not yet break out .Net version info.