Ex-SMS Ostfriesland in the 1920's tests undertaken by the US Army air Service and USN suffered relatively little damage from the direct hits inflicted on her, but suffered extensive damage from near misses that in fact ultimately caused the target to sink.
Merchant shipping affected by near misses usually suffered fatal damage from such strikes. If the ordinance was a torpedo fitted with a magnetic pistol, an underwater detonation that didn't actually hit the target was usually more damaging than an actual hit.
Depth charges worked almost exclusively on proximity concussion effects to sink submarines, and on several occasions sank escorts and merchant shipping as a result of proximity detonations. Later DCs were fitted with hydrostatic switched designed to prevent detonations above 60 feet depth.
Unquestionably near misses were potentially the most dangerous form of hit to all forms of shipping
Also there are many reports dealing with damage on ships, including damage sustained from near misses. This particular report is from DNS, concerning the bomb damage inflicted on the HMS Indomitable in August 1942.
Bombs dropped by skip bombers usually had a 4-5 second delay. This gave the aircraft time to clear the blast zone and had the additional effect that a near miss detonating beneath the ship's keel would break its back.
Aside from the water hammer concussion effects, the riddling of lightly plated parts of the hull and topsides by fragments could cause significant damage. It was not unusual for topside exposed crew to be killed or wounded by near misses. I don't think that skip bombing was attempting to explode a bomb under the ship, but to impact the sides of the hull above waterline.
The Fletcher Class Destroyers had 20# (1/2") STS plating by way of machinery spaces as some help against near misses and strafing.
A direct hit was the desired result, but near misses were still dangerous. General Kenney instructed his level bombers to use instantaneous fuses, rather than the standard 1/10 second delay, to increase the shrapnel effect of near misses.
During the war ships underway were very seldom hit by level bombers. A Japanese Destroyer sunk by such a hit had it's Captain complain that even the B-17's got lucky now and then.