I already own the Steam version of Wizardry 7, but the game window is really small.

In the GOG version can I scale up the window?

Yes.
At least the DOS version you can scale with DOSBox. Not sure about Wizardry Gold, but the Gold version is inferior anyway.

Ummm, I am referring to the Gold (Windows) version. So far I know that it also contains the clue book.

The only way I know of is to set the executable properties to use 640x480 resolution. Find where it's installed, find the .exe for the game, right-click it, go to "Properties", and go to compatibility settings (name varies depending on your version of Windows). One setting should be to set for the above resolution (which is what the game runs at if IRC). That should make the game take the entire screen. Your mileage may vary if you have a widescreen monitor. Good luck!

References :
Vista / 7 : http://www.howtogeek.com/howto/windows-vista/using-windows-vista-compatibility-mode/
8 : https://www.maketecheasier.com/windows-8-compatibility-mode/
10 : (second section titled "How to Run an App in Compatibility Mode") : https://websetnet.com/how-to-set-compatibility-mode-for-apps-in-windows-10/