I've read that report a few days ago, as it was a 47 Ocean, so close relative of our 40 Ocean. Except we don't have the big windows that broke. According to the report, they shattered outwards due to hull flex, so they must've been glass windows. We don't have any glass windows except for the windscreen, which is outside and won't flood the boat when shattered.
The open hatch is a bit of a mystery. The report didn't say why it opened, but it said it was found open after having been closed, rather than ripped off. So I suspect it maybe wasn't locked, in which case wave pressure could have opened the exterior handles. Our exterior handles disappeared in a storm[1] where we had rammed the bow under water a couple times, but since the inside ones were locked, the hatch was fine. The water pressure was strong enough to tear off epoxied handles, so it would easily be strong enough to turn unlocked ones to the open position.
The hatches on the Oceans were either Rutgerson or Gebo, and from the pictures I've found of Essence, it looked like Gebo (same ones we've got). The Gebo hatches are pretty well designed and strongly built and I'm not too worried about them. In the aforementioned storm, our forward one let in a few drops of water through the seal as we had waves on the foredeck and like I said, the exterior handles got torn off and disappeared, but the hatch was locked and I doubt it would open. Most likely they forgot to do that, perhaps out of habit. The usual fallback for dealing with a smashed hatch would be to screw one of the plywood locker tops over it, but in reality I think it would be near impossible to do that on the foredeck in those conditions - same reason the crew of Essence didn't install the storm covers they had aboard. You'd be under water a lot of the time and powertools wouldn't work even if you could go and find the right tools and materials while being tossed about in the cabin.
The autopilot (with the upgraded added gyroscope box) copes fine and the drive has plenty of power, but that doesn't matter, because you will need to helm manually in those conditions with any autopilot in the world - none of them have eyes, and you need to steer up and down the waves yourself or risk smashing into a valley. We did fall down into the trough a few times (whenever my sunglasses were encrusted with salt and I couldn't see without them due to painful water particles driven in my face by the wind) it was very a scary bang with just 4m waves - the crash is epic and I can totally see the hull flexing enough to shatter the big glass windows on the 47 Ocean. So this must be avoided by steering up the waves at an angle and then straightening up at the top so you don't broach in the bottom, and the autopilot can't do that.
Wind strength doesn't really matter until it gets over 60 knots sustained, which is rare. Then it starts tearing bits off the boat (solar panels, canvas, unsecured sails, etc.) and most of those you can secure beforehand. It's the waves that make all of the trouble. For wind, you reef deeply or sail barepoles to your liking. Reef early, and learn how to do it without turning into the wind, as that won't be possible. The other time we had to sail in a storm was in last years medicane, going from the Othonoi islands north of Korfu to the SE corner of Sicily. We were in the NW quadrant of the storm which was going eastwards - it wasn't too bad, wind was only 40-45 knots and we had a scrap of mainsail out (perhaps 1-2 square meters, just a bit more than the furled in main would be) and surfing down big waves at 7-8.5 knots with good control and still under autopilot this time (there was a good bit of current going with those waves, which helped lengthen the intervals). The Genoa would've been better, but it didn't really matter and you don't make changes in those conditions if you don't need to - just more risk of something going wrong.
Waves are hellish, especially in the med, where they come at very short intervals and with very steep fronts. At more than 3-4m wind wave you won't be making much progress upwind and will have a horrible ride in a 40 footer. In the Atlantic where the waves are further apart, this is a different story, but even their eventually your best choice is to turn around, go downwind, enjoy a vastly smoother and safer ride and just get back on route when it's all blow over - assuming you've got the room to do that.
A point panicked skippers often forget is that it's much more dangerous to try and enter the wrong harbour in those conditions than to ride it out at sea.
As for a drogue, the widely agreed best solution is a Jordan series drogue attached to very well reinforced strongpoints at the stern. We don't have one as it's a bit pricey, but I'd probably take one across the Atlantic if we ever end up doing that. So far we haven't missed it!
We can resort to towing a few loops of thick mooring lines in lieu, but never had to do that.
The drogue would be deployed when the waves are getting too big to surf down under control. And in a big storm with sufficient seaway, I'd always be sailing downwind, it's by far the safest thing to do with our kind of boat. That's the general recommendation from the Heavy Weather Sailing book too (which I recommend reading based on the questions you're interested in).
[1] I blogged about that storm here:
https://sdfjkl.org/blog/2019-04-09-gale-at-sea/