Thank you for posting the link to that article. Despite the fact that it's a media report and could have errors (there are typos), this paints a reasonably clear picture of what happened.
As others have mentioned, it is not necessarily a problem to have a transom cut-out (or even a completely open transom), or numerous scuppers or freeing ports (slits in the sides of the boat at deck level which can let water out -- or in) --- as long as the boat is properly designed (and maintained) for it.
As a more extreme example: Sailboats commonly heel over to the point where they are basically awash. Even when they are not heeled (i.e they are upright), the cockpit and decks can be repeatedly swamped by waves. And yet they survive. Now the reason they come back to vertical is mostly because they have ballast; but the reason the water does not pose a problem is because they are essentially "sealed." They also have drains (sort of like freeing ports in function) and bilge pumps, but those would never have the slightest chance of keeping you afloat if the boat's "seal" were breached. After all, there may be 4000# pounds of lead in the bilge of a 30' sailboat, and yet they take on "green water" all the time without sinking.
So, if you had a hatch (cabin entry) board out, or a cockpit locker that came open (these should be very securely dogged).... forget it. You would be in serious trouble, even with three bilge pumps, and four drains, you would sink. Just like the story I wrote back in the beginning of the thread where a 3" hole in the boat caused it to nearly sink (and if we had been out on a reef we would have gone down quickly). No bilge pump can keep up with that.
BUT, as long as the interior of the boat (in this case meaning below decks) is a "sealed box" --- even if you have an open transom --- it will be fine (okay, presuming it is designed that way; for example on a simple open skiff with no flotation, of course it would sink without a transom, because there IS no "sealed box" for buoyancy). Essentially, you have buoyancy to keep you afloat as long as there is air in the boat. That's how an open transom boat can be fine. In fact, it lets any water that does get aboard drain much more quickly, which is a huge plus --- as long as the "below" is sealed.
Speculation:
Without seeing the boat, I would say that a hatch leak in and of itself would not necessarily have resulted in the same outcome. Because a bit of "drizzle" or even a small stream of water would probably not overwhelm the boat (it could, but doesn't seem that likely from what I can tell). But, reading about the hatch-with-attached-bench that (seems to have) floated free and trapped the two divers, I'm thinking that perhaps it was not secured (i.e. fastened closed in a positive fashion).
In this case (and don't we know how this goes) it seems like it was a combination of problems. Here is how I can imagine it happening (i.e. I'm speculating):
1) For some reason, some water gets into the bilge. Maybe it comes in through the leaking hatch, or maybe there is another leak source. If bilge pumps weren't working, this water could slowly build up in the hull.
2) Boat goes to leave site (may or may not know about the in-hull water at this point). Divers are in the cockpit, adding weight. They throttle up, and (as is normal) the bow comes up and the stern goes down. Any water in the bilge rushes to the stern. At this point two things may happen:
a) That water rushes back and up and dislodges the bench-laded-hatch from below. Now you have a giant hole in the deck.
b) At the same time, the increased "down by the stern" allows water to come in the open transom door.
3) Now you essentially have an open boat that is swamped. More water depresses the boat more, allowing whichever one of (a) or (b) that did not happen before to happen now, and you are sinking/sunk.
4) The boat remains upright as it sinks, and the bench-laded-hatch floats forward (or in some direction) and traps the two divers (maybe under the mini-roof that is over the cockpit).
Okay, but replay that (speculated) scenario but eliminate some of the factors.
1) There is a leak while they are diving, but the bilge pumps are well-sized and are working. That may be enough to stop the spiral, and they get back to the dock and figure out what's wrong so they can fix it.
2) There is a leak while they are diving, and the bilge pumps are NOT working (or are inadequate even for "nuisance" leaks), but the hatch is dogged (fastened) tightly. They might still go down by the stern enough to allow water in through the open transom door, and then sink, but it would probably take longer, and there would be no bench-laden-hatch to move and trap anyone. It's more likely everyone would have gotten away from the boat.
3) There is a leak while they are diving, the bilge pumps are not working, AND the hatch is not secured, but the transom is "closed." They might still sink (water can come in the freeing ports and eventually over the gunwales themselves), but this buys people time to get off/away.
4) There is a leak while they are diving, the bilge pumps are not working, the transom is open, but the hatch IS secured. In this scenario, they could still sink, but not until they took on quite a bit of water from the leak (either a leak from below or water getting around a leaky hatch) again it seems to me it would be a much slower event, and with no bench-laden-hatch to trap anyone.
Blue Sparkle
Edited to add:
I originally said this:
Despite what look to be a few typos (for example, when they say the hatch did not "flip," I'm wondering if they are talking about the boat itself staying upright),
As I think about it more, they may be saying that the hatch did not "flip" in the sense that a hinged hatch lid "flips open," but instead simply "moved over" off it's hole, and trapped people that way (plus exposed a large hole in the deck). OTOH, since they aren't clear, maybe they were saying that the boat did not "flip," but instead sank upright, since initially it might have sounded like it turned over and trapped people under it. I just wanted to edit to reflect this. They could have written more clearly, of course! The boat sinking upright-ish seems probable to me, given the design and the fact that otherwise the hatch might have sunk "free" of the boat/passengers.
