Omitting the article in question would be the way to go. You are correct in your first guess's analysis that the reason is because we're not talking about any particular creatures; rather, we're just talking about creatures generally.
The fact that the creatures are specific to Earth doesn't immediately change that basic interpretation just because "on earth" is included in the sentence.
The sentence is still intelligible with the second "the" in there, but it's a bit clumsy.
That said, your second interpretation about contrasting Earth's creatures with creatures on some other planet brings up an interesting possibility for including the second "the" in a more idiomatic way.
Let's imagine there is another planet, Vulcan, that has millions of creatures of its own. Let's further imagine that somehow the people of Vulcan manage to meticulously keep track of exactly how many of each creature is living on the planet at any given time.
If we wanted to compare the total number of creatures on Earth to the total number of creatures on Vulcan, we could say
It is very difficult to point out the number of creatures living on Earth. But we know there's exactly 1,243,823,843,043 creatures on Vulcan.
Now let's imagine that among the creatures on Vulcan are dogs. We know there are tons of dogs on Earth, but we don't know exactly how many. Vulcan, though, knows it has precisely 343,875,932 dogs.
Say we're talking about dogs and how there's a whole bunch of them living on both Earth and Vulcan, but because Earth doesn't keep track of exact numbers like Vulcan does, we would have trouble giving an accurate total number of dogs. Then it would be correct for us to say that we can't get an accurate total because
it is very difficult to point out the number of the creatures living on Earth.
In this specific context, the emphasized "the" refers not to all creatures on Earth, but to dogs in particular.