I would be really interested in hearing more about this (noob in this area). Are you saying the old Nikon / Canon lenses from 90s are a bad choice for modern DSLRs from these companies, or did I completely misunderstand you? If so, why is that?
Using an older lens with a camera sporting a 20+ MP sensor will give you less sharp results than a similar new lens. But the image will be no worse than that old lens shooting film. And the lens will be much cheaper!
If you (or others) like the results, the technical details do not matter.
If a digital SLR and a light table can get you enough resolution for what you want to use the images for though, that's fine. You could use that for most of your images and then get the ones you want to print really large professionally scanned later.