Passwords are not saved in shortcuts created within SAPGUI. In fact, when you edit a shortcut, the password field is grayed out.
Why? Because you need to first register the SAPshortcuts using the following:
SAPSHCUT.exe is located under the SAPpcsapgui directory, but in SAPGUI 4.0 it was called SAPSH.exe.
Once you do the registration, you need to open the registry (regedit or regedt32) and change the value data of "EnablePassword" to "1" under the following:
Then, you'll be able to type and save your passwords.