You might do some comparison testing both with and without the borders, paying critical attention to image contrast. The light shining through the sprocket holes can sometimes cause slight veiling flare and reduction in contrast, depending on what lens you are using to copy the negatives. Hopefully, that will not be a problem for you, but I would want to rule it out before spending a lot of time digitizing a shoe box full of negatives.
It can be time consuming, but I prefer to edit the metadata for my scanned negatives to include the film type, and other analog details. One advantage of having the film details embedded in the EXIF metadata, is that it becomes searchable on your computer.