You can disable the system beep function in client rdp sessions by creating the following registry key on the Terminal Server:
add a DWORD “DisableBeep” with a value of “1”
You will have to restart the Terminal Services service for the change to take effect.
The above applies to Windows 2003 SP2 and Windows 2008. If you are running Windows 2003 SP1, you will need a hotfix first: 901115 – A Terminal Services client computer may make beep sounds after you connect to a Windows Server 2003 Service Pack 1-based computer