FWIW - I have always found that my scanner can see and record the grains of silver in my 35mm B & W negs, which to me is not very nice BUT my 8 x 10 silver prints (made in a darkroom) produces beautiful smooth looking images with barely perceptible grain. I would assume that something similar might be happening with your scratches; i.e. scanners tend to be unforgiving and sometime too sharp for their own good. I seem to recall reading an article somewhere on the net from a shooter in Scandinavia, I think, who wrote about reducing resolution to a point he worked out mathematically to avoid that issue. But for the life of me I cannot recall where I saw this........ sorry.
cheers,
Sam