As for some of the questions, there IS oxygen on board the Sakura. The profiles can be very deep so this is absolutely necessary though we were told in 12 seasons they have never needed it (knock on wood). We also had 12 divers on board (plus 2 divemasters and 6 crew - everyone sharing the 2 toilets and one shower) even though it is advertised as 11 - the most fore-cabin should likely only be a single. It has a double bunk but is quite a tight squeeze and has no porthole so can get quite stuffy in there.
The seals on most of the hatches are not air-tight and this was certainly cause for a lot of the leaking. During the crossing, I went down to sleep in my bottom bunk where it was dry-ish (I am not so prone to sea-sickness though several guests were very sick and not really looked after my staff - luckily fellow guests stepped in) but my feet kept getting splashed despite the hatches being closed. In one of the two compartments for bags, the left-side's lid was flipping up every time the boat hit a wave (so was easily flooded) - the other compartment didn't behave that way but was obviously still leaking as evidenced by my ruined bags which will now sit in a fresh water soak for some time.
Tubbataha is sooo good that I can't say it was a nightmare or that my experience was ruined. We regularly came up from our dives just gobsmacked - they were busy dives too as in one moment you'd be swimming alongside a big whale shark only to be distracted by loads of (pretty big) reef sharks, huge schools of jack/tuna/barracuda etc, only to run into some hammerheads, mantas - this place is crazy. Even a terrible boat can't ruin it (though admittedly a lot of it has to do with luck - we had two tenders on our boat and I was on the lucky one, though I think our DM was a bit more tuned in to where to go and when to find the big guys so not entirely a question of luck - and you have to go deep - the other boat saw a single whale shark the whole trip and no hammers or mantas - we saw whale sharks every day and all of the other goodies too - and regularly). Lesson learned though - spend the money for a good boat and then the top-side experience can be just as good as the diving.