Had a similar problem years ago with an Aquatica zoom ring and a Tokina 10-17 lens where the zoom ring did not fit tight enough to prevent slippage UW. I installed three small set screws 120 degrees apart on the zoom ring. I positioned them to contact the zoom ring in such a way that they met the lens rubber zoom adjustment at a solid part of the lens. It was some years ago, but I believe they were 6-32 with an allen head. I bought a 6-32 tap and handle, about $10 back then. The biggest trick is to make sure that you drill the holes for the tap the proper size. Also pick the length of the set screws so they are flush with the outer portion of the zoom ring when tightened. And make sure that the set screws are positioned such that they do not interfere with the housing gear as the ring rotates.
I have since installed set screws on all of my zoom rings and have not had any slippage problems since.
For years, I have used a bag in a bag approach to checked luggage containing valuable items, i.e., housings, strobes, etc. I pack a sturdy, reinforced carry-on size bag inside a non-descript, well -worn duffle bag, so it doesn't scream "valuable items inside" as a Pelican does. I use my tee shirts, swim trunks, etc. as padding. Never had a problem as it seldom gets looked at by TSA.
But I have never packed cameras or lenses in this manner. Those are always in my carry-on. If this new policy becomes more widely implemented, going to have to give this some thought.
One question: Do we know yet if the current policy from the Middle East includes lenses? My reading of the restrictions is unclear.
Also time to review my insurance policy for such items. BTW if you're eligible for USAA insurance, they have an All-Risk personal property policy that has zero deductible. And it's very affordable. I had a mechanical failure on a D70 housing years ago and they paid the claim promptly with few questions.
You'll find as many opinions on manual vs TTL as there are days in a year, maybe more. When I was just starting UW photo, I found TTL to be useful in some cases, esp. if you can adjust the exposure on your camera by shooting in manual.. Now I shoot about 30% TTL and the rest manual strobes. Use TTL mostly for macro. I'm not familiar with the SS-2. I use the D1s and love them.
Here's a long shot to consider. I don't have a D800, but do have a D500 and I assume that the menus are similar. If the delay is consistent in length, there is a setting in Custom called Exposure Delay Mode. It's d5 in the Shooting/Display menu on my D500. I's assume that it's also on the D800.. If that is set to other than off and is somehow getting triggered while UW by pressure, that may cause the problem. This is different than Timer Release. Like I said, this is a real long shot.
Also try this. Make sure that you're using AF-C focus mode and set the a1, AF-C Priority Selection to Release. This will cause the camera to fire without the need to achieve focus. If this eliminates the problem, then the camera is, in fact, waiting for focus before firing and, for some reason, it taking an inordinate long time to get focus.
Like the others have said, misalignment is the most likely cause. The trick is to figure out which button is getting pressed to cause the problem.
I'm not familiar with the S&S housings, but I had an old Aquatica D70 housing that had plastic thread protectors on the end of the rods used to activate the buttons. Occasionally one of those protectiors would work itself loose and contact a button before it was intended to do so. This drove me crazy until I figured that just a slight amount of sea pressure on a button would cause contact with the button when the protector was slightly out of place.
Reef Photo isn't too far away. Consider taking the rig into them for a look.