I think that there were a lot of Ju 88's used for antishipping in level bombing around North Africa, but they did bomb from lower altitude.
There is a huge difference in ability to hit a ship between one that is maneuvering and one that isn't (or is just put into a predicatable turn before the bomber has even reached its drop point). We see this in scenarios -- ships maneuvered by a human watching the action and maneuvering to make bombers miss are much, much harder to hit.
Here's an example of ship that would have been obliterated by B-17 attacks (bombs quite well placed, looks to me) if it hadn't been quite adeptly maneuvered.
(Image removed from quote.)
Your picture shows one glaring fact... it all depends upon your perspective. From 25,000 feet they look pretty close......BUT:
Hiryu was 728' 5" long at the waterline. The
CLOSEST bomb splash in that particular picture, around two boat lengths away... most are further. So, the closest splash to the Hiryu, around 1500 feet. I guess hitting within a quarter mile of your target is good (Horribly ineffective, but good)...actually about the average in the war.
Hitting moving ships with large level bombers is asinine...they lacked the maneuver capability to keep up with one turn of even the largest ship. It took 68 Lancasters to get 2 (Possibly 3) hits on a
stationary Tirpitz in Tromse, in two separate operations (
"Obviate" and "Catechism") FYI: The Tirpitz was 40 m longer than Hiryu.