I would go with E. I narrowed down to A and E using a split. B, C, and E sort of change the meanign at the end of the sentence.
It is well known in the supermarket industry that how items are placed on shelves and the frequency of inventory turnovers can be crucial to profits.
(A) the frequency of inventory turnovers can be
(B) the frequency of inventory turnovers is often
(C) the frequency with which the inventory turns over is often
(D) how frequently is the inventory turned over are often
(E) how frequently the inventory turns over can be