What I usually do (brute force method): create a replacement logo, or just a tiny, blank gif file to use as a placeholder. Name the file logo_phpBB.gif.
Upload the replacement file to phpBB2/templates/subSilver/images/logo_phpBB.gif,
overwriting the existing logo file.
If you create a viewable replacement logo, life is easiest if you make the image the same size (200x91) as the existing logo. If your replacement is just empty space, you don’t have to make a big file; just a single transparent or background-colored pixel will do.
I prefer to simply swap out the default logo because all that’s involved is uploading a single file; no edits to any code are necessary, so later version updates are a breeze.