They could have just ran those apps in compatibility mode, which returns different values for all the GetWindowsVersion calls.
Or they could rename the entire OS.
Or they could rename the entire OS.
So I don't buy this rumor at all. The number of real applications that 1) remember Windows 9x exist, 2) aren't completely broken on modern Windows anyway, and 3) go out of their way to use some convoluted version checking method has to be extremely small.
[1] https://searchcode.com/?q=if%28version%2Cstartswith%28%22win...
[2] http://docs.oracle.com/javase/tutorial/essential/environment...
Python for example wraps GetVersionEx appropriately with sys.getwindowsversion()