So ... I removed my Sims 4 folder, started a new game and let the Villareal household buy a premade shop in Magnolia Promenade. The bugs remain exactly the same:
While shop is open:
Household members restock all goods except mannequin outfits -> No effect in the shop management panel
Household members restock mannequins -> Costs (175 $) are shown correctly in the panel. But the "flying red 175 $" in the air is immediately overlapped by a "green 175 $". If your Sim has the wealth aspiration, restocking a mannequin will thus be shown as earning in his aspiration panel
Employee restocks goods -> Restocking costs are shown correctly in the shop panel
WHEN YOU CLOSE THE SHOP -> only your employee's salary is taken away from the profit. Restocking costs are shown but have no effect on the overall shop budget. When you re-open the shop the next morning, they are simply reset to 0.
While shop is closed:
Restocking by your household members is for free, no effects in the shop panel
So in my game the retail system is completely broken.