Best way to fix those piping holes is to cut wood plugs from the same material. Glue in place with a GOOD quality wood glue or wood patch. Let dry, sand and varnish or paint.
This is a teadish job but if done correctly should look like a knot in a tree and should BLEND in with the remaining ORIGINAL floor.
I never recommend PAINTING OLD hardwood floor ad these material are really hard to come by in todays market.