For flies, I feel it only makes a diff if they swallow the hook a lot. I guess the same holds true for bait, but that's not in question here.
I fish crab flies alot, and the bass get them to the crushing plates in the rear of the throat right away. Thus I have experienced a higher number of deep hookings with crab flies than with sand eels or juvies. There might be two reasons - (1) I am moving the fish flies faster (2) the reason I theorized above.
I even tried setting as fast as possible but still got some deep sets. I am trying circle hooks for crab flies this year, will let you know!