I would say it's just nuance:
If you're starting talking about all animals in the world, or a specific group, 'which animal is the fastest/tallest?' is good because THE fastest/tallest is very specific, however,
continuing the conversation with more superlatives, there's no need to be as specific each time; 'And,.. which (of them) is fastest/tallest/cutest?, etc'.
You can say THE each time, but it seems to emphasize that each is special.