Bo Peep's Shear the Wool ability says: "In each Roll Dice step, for each purple or blue miss rolled, +1 gold."
Shellduun's during effect says: "In each Roll Dice step, change all rolled basic hits to misses (if possible) and all rolled crits to basic hits." For this effect and similar ones, the changed results do not count as having been "rolled" for Bo Peep's effect. So she cannot gain gold for blue and purple dice that were rolled as basic hits and changed to misses by Shellduun.