Tony,
Stopping down the lens makes the hole the light is passing through on the way to the film smaller. This has two important optical effects besides reducing the amount of light getting to the film: 1. the smaller the hole, the greater the depth-of-field. 2. the smaller the hole, the more (image-degrading) diffraction there is. Further to this latter: there is a "sweet spot" in most lens designs where stopping down eliminates lens-design flaws and aberrations, but where the image-degrading effects of diffraction are not yet enough to really reduce image quality. Any larger aperture and there would be more degradation due to aberrations; any smaller and diffraction would degrade the image more. This point is different for different formats; for large format it is approximately f/22.
Neutral-density filters reduce the amount of light getting to the film by absorbing some of it on the way through the filter. This is independent of the effects of stopping down. Using an ND filter to get the same exposure at f/5.6 as you would get by stopping down to f/22 retains all the optical characteristics of an f/5.6 aperture, i.e., shallower depth-of-field and possible degradation due to lens aberrations (which would be corrected at f/22).
So, you can use an ND filter to get the right exposure with an aperture-less f/5.6 lens, but you'll have to live with the optical effects of the larger f/5.6 aperture.
BTW, you don't have to focus with the ND filter in place...
Hope this helps,
Doremus
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