Dave,
I haven't had a chance to confirm whether or not the silent install skips the web access installation, but I can tell you that there is a seperate installation for it that is kicked off. The setup file is located under \syslog\setup\ after you install the Syslog server.
I would also make sure you manually stop the kiwi service if it exists prior to reinstalling. The only issues I have had with installing a new version over an older version have been with the service failing to stop when setup tries to do it.
And last but not least, I don't see anything wrong with how you're getting your version numbers personally. Getting the current version from the registry is pretty much right out of the book and as long as they don't change their naming convention, getting the new version from the filename is really the only place I can think of to get it short of digging through the setup file itself.