Off the top of my head,the Essex of course suffered exactly such a penetration at Fort Henry with 11 killed and 23 wounded be the escaping steam, including Porter who was blinded (temporarily as it turns out) amongst other injuries. The Mound City had only 26 survivors out of her complement of 175 when a boiler was penetrated on 17th June 1862 (although only 97 of these were killed onboard, many of the rest died in the water as they came under musket fire).
I'm sure there are other examples, but the Essex was completely rebuilt, this time with the boilers below the waterline. The danger of exposed boilers was revealed, and was a nightmare that no captain wished to face. Hence the Captain of the Kearsarge trying his best to prevent such a hit.
The positioning of the boilers had a serious impact on the survivability of a ship under fire. A vertical boiler was such a hazard that essentially no RN ship had one. Some USN ships certainly did, but certainly the Merrimac's had the boilers well below the waterline to be survivable.
ok, the
Essex is exactly a 1000 tons, so somewhat meets the definition. However, she was shallow draft and essentially a single decked river boat with armor on it. Any conventional deep draft ships with multiple decks?
We are focusing on the war at sea, while riverine warfare has its own special conditions (the shallow draft requirement being utmost).
Regarding the Kearsarge ... this is what wikipedia says, but I have seen this exact quote in other works and it is quoting (in fact the wikipedia post is nearly word for word) from The Dictionary of American Fighting Ships Online
"This hull armor had been installed in just three days, more than a year before, while
Kearsarge was in port at the Azores. It was made using 720 ft (220 m) of 1.7 in (43 mm) single-link iron chain and covered hull spaces 49 ft 6 in (15.09 m) long by 6 ft 2 in (1.88 m) deep. It was stopped up and down in three layers to eye-bolts with marlines and secured by iron dogs. This was then concealed behind 1 in (25 mm) deal-boards painted black to match the upper hull's color. This chain cladding was placed along
Kearsarge's port and starboard midsection down to her waterline, for the purpose of protecting her engines and boilers when the upper portion of the cruiser's coal bunkers were empty. This armor belt was hit twice during the fight: First in the starboard gangway by one of
Alabama's 32-pounder shells which cut the chain armor, denting the hull planking underneath, then again by a second 32-pounder shell that exploded and broke a link of the chain, tearing away a portion of the deal-board covering. Even if the shells had been delivered by
Alabama's more powerful 100-pounder Blakely pivot rifle, the impacts were more than 5 ft (1.5 m) above the waterline and would therefore have missed her vital machinery."
This implies that her vital machinery was below the waterline
Apparently that chain armor was a bit more effective than one would think