The scanner feedback parameters are what is causing the beep you are hearing now. This parameter is set before the barcode is scanned, so you will not be able to control it based on what type of barcode is decoded. As you have seen, that beep happens as soon as the scanner decodes the barcode (before the event is triggered). You can disable that and make your own sound if you want, but there will likely be a noticeable delay. What might be better is to try adding a second beep (or other sound) when you see that the barcode was a 2D. I have seen where customers use a second beep that is a different frequency to indicate something to the user.
If you want to disable the feedback beep, I think this would probably do it. You would do this after you create your reader and before you start a read.
myReader.Parameters.Feedback.Success.BeepTime = 0
If you want to play a sound on your own, look at the audiosample app on your PC. This shows how to do either a beep or play a wav file.
C:\Users\Public\Motorola EMDK for .NET\v2.9\Samples VS2008\VB\VB_AudioSample1
If you have problems playing a second sound after the original feedback sound, I seem to remember sometimes there being issues where the audio hardware might still be busy after doing the sound from the scanner, so would sometimes fail to play a second sound, but I think this might have only been if you use .wav file (not a beep).