Ok, the next way to do it would be with Windows API calls. There are API calls GetFileVersion (or GetFileVersionInfo).
However, there's no SetFileVersion API call. Well, at least I didn't find anything like that.
Finally I found StampVer, a freeware utility to change version resource of a Win32 executable (there may be other similar tools). Since it seems quite impossible to use VB.NET directly, could it be possible to use a third-party tool. Now you could call the utility with Shell or use System.Diagnostics.Process class.