USS Hammann was guarding the Yorktown when it was torpedoed along with the carrier. In a tragic irony, many of the Hammann’s crew were killed in the water when the sunken destroyer’s depth charges exploded.
IJN Mogami and Mikuma are an interesting contrast. Wary to the threat of further air attack, the Mogami’s damage control officer had ordered the cruiser’s torpedoes jettisoned, over the angry objection of the ship’s torpedo officer. When the next wave of bombers hit, both cruisers were attacked...and the Mikuma took a hit amidships that detonated its torpedoes, fatally crippling the cruiser.
The Japanese Navy had an interesting (and strict) protocol of priorities for torpedo use...IIRC cargo ships were to be attacked only if no warships (i.e. a more worthy target) were in the vicinity, and then only one torpedo was to be expended on a cargo ship. Even with that, like you noted, many (but not all) Japanese sub skippers passed up easy merchant shipping targets in anticipation that they might find a “worthy” warship later on.
In addition, a destroyer rated one torpedo, a cruiser two, and no more than three for a battleship or carrier.