I understand your question quite clearly.

I believe part of the reason is the common statement people say against the Noah story.

"How did he fit ALL the animals in the ark"

The fact that many animals today are gone could mean exactly that Noah was NOT able to take all the species in the ark.

That would include the bird dinosaurs, afaik, birds are not capable of flying 24/7 for a whole 1 month. It's not like they could all find Noah's ark and stand on top of it either, and I don't think Noah would give them food if it is rationed enough to just feed the animals already in the ark, they may have also been used as food for other animals, the same for other aquatic animals, they may have fished for food and thus the only food they had to have instock are vegetable hay etc.

The aquatic concept is interesting that you said that cause I was thinking about that for a while now.

Did you know that there are places underwater that we haven't explored yet? Many sea creatures live there that we haven't even discovered yet.

Also only recently have the sea scientists found many things thought to be extinct, theres also the giant squid 150 ft long that they haven't even thought could exist.

OK other reasons.

-Food Shortage. Climate change- temperature etc. Salt vs Seawater etc.

I believe that those creatures may have actually survived but died out later on.

Such large creatures would require large amounts of food. There will be great competition and only a few would survive.

One factor you didn't include is the concept that back then, there were probably seas but not oceans.

Think about how much would change in your theory if you put that into account. The concept of the creationist's view on this topic is that back then there were more land on the surface and most of the water we have on the oceans back then were under the soil, until the time came when the Bible said "the fountain of the deep broke open"

I believe it speaks of the ocean ridges (you can see giant cracks on the earth underwater.

anyway, the food scarcity in this new huge ocean would have been problem for lage animals and they would have to compete with the whales. I believe the whales got lucky.