Regarding the story of the flood: If God flooded the Earth, all the land mammals and insects would die, but not the sea animals. Maybe some of the birds would survive. Isn’t this unfair and needlessly cruel? Why would God destroy innocent creatures like deer and rabbits but leave sharks and killer whales alone? And if all the land animals were destroyed and then had to start over, wouldn’t there be way more sea animals than land animals today?
There is a range of ways to understand the flood story, and my response to your question would be highly dependent on one’s view of the flood. Some claim that the flood is a mere myth, with no historical reality. I completely reject that interpretation, both because of the cultural evidence for an ancient flood and because the Bible is inspired by God.
Some claim that the flood was total in its effect, but only locally—in Mesopotamia. This is called the local flood theory. I am very doubtful of this interpretation because the story itself, with its abundant use of the words all and every, plus Jesus and other Bible writer’s comments on the flood seem to make this interpretation unlikely. Plus, science and the law of gravity seem to preclude a massive 150-day flood in Mesopotamia not being dissipated more widely. If this second interpretation were correct, then your question would be more or less meaningless.
A third interpretation is the one I personally favor, which is that there was a miraculous massive outpouring of rain and water, and it affected the entire earth, but it did not literally cover the entire earth up to the top of Mt. Everest. The “more than 20 feet” of water might be the amount of water that fell generally, not the height of Mt. Everest plus 20 feet. This seems to me to be the most likely scenario for the flood. If this is correct, then, although many creatures were indeed saved on the ark, along with Noah and his family, there would have been remnant populations of most species across the earth, on every continent. The remnant populations could then repopulate the areas devastated by flood.
The fourth possible interpretation is that literally, the water rose above the top of all the mountains—perhaps above Mt. Everest, or more likely above the highest mountains of Ararat in the area around Mesopotamia. If this scenario were correct (and it seems to be the one you are assuming to be correct), then your question does in fact come into play. Be aware, though, that this is not my preferred understanding of Genesis 7. However, let me respond to the possibility, both because it appears to be your understanding, and because I will admit that it may be correct and my interpretation may be wrong. If a flood literally covered all the land on the earth, then many, many species would have been completely wiped out. Duck-billed platypuses and Tasmanian devils, armadillos and llamas probably did not travel to Mesopotamia to get on the ark. If we accept this scenario, then I suppose we will need to believe that God somehow recreated these species after the flood in order to repopulate the earth.
Your question seems to imply that you think that “innocent” deer and bunnies are “good” and sharks and killer whales are “bad.” I do not agree with this. After his creation, God called all of his creatures and all of his creations good. In fact, he called them very good (Genesis 1:31). I do not agree that it would be somehow worse for bunnies to die than sharks. Sharks are good. Killer whales are good. Oak trees are good, and bunnies are good because they are part of nature and all of nature is good. It is not evil for a lion to kill an antelope. They are only doing what is natural and what is natural is good. It is all a part of the wonderful, beautiful and amazing creation of God. Also, once populations were reestablished, within just a few generations, the land animal populations would repopulate the earth. With exponential growth in populations, with sufficient plant life to eat, land animal populations would come into balance quite quickly, so that the relative overabundance of sea life you anticipate would disappear within a couple of centuries at most.
I hope this helps.