I cannot verify this since I can only VPN in to work, but in 8.2, the Beep.vi function has an input called use system notification. When True, I know it is using the sound card cause it gets sent through my Remote Desktop connection. When set to False, I don't hear anything, so it is not using the sound card. Now, whether or not it is using the PC speaker, I cannot say. You may also have to play with the other inputs to get it to work (freq and duration).
If that is not working, then try the Windows API call Beep (
http://msdn2.microsoft.com/en-us/library/ms679277.aspx). It uses the speaker in Windows 2000 and later, but is not supported by Visat 64-bit. It claims to not use the soundcard (Win 95/98 uses the sound card if installed, otherwise uses the PC speaker).