It depends on whether the rods are steel or aluminium. Stress raisers should be polished out of aluminimum, and ground out of steel rods. It is pointless shot peening aluminium rods, with steel rods the peening creates a surface layer which has the effect of distributing the stresses . Japanese two stoke rods often dont have the marks ground off them, they are s hot peened then copper plated. When I built my methanol fueld T250 Suzuki, I balanced the rods end for end, by grinding weight of the little end of one of the pair , then I polished both. It was not good practice to remove the shot peened layer, however the rods did not fail in that motor, and after I sold it, the next owner won 28 races and five historic championships, with that bike. The Suzuki rods I used were from the T20 model which had smaller little ends, gudgeons etc, and supported a piston with a wider skirt on the inlet side, so the inlet ports were widened a lot.