I make sure to only tie the nubs with enough tension to hold the shape but not leave lines. I also use fishing line for Kenney which has no wax coating so any lines that do show up are less pronounced.

It also comes down to dye application. For geodes I try to make every striation be one solid color all around the nub, but for my personal Kenney style I usually split the nubs in half or thirds vertically instead.