A quick Google of "1 million population" shows that it is done without the hyphen. You can use numbers or words for numbers, just make sure your usage is consistent. You probably wouldn't want to use 1000000 though because it could be hard for some readers to determine how many zeros there are.

It's a question of style rather than grammar whether to use hyphens with compound adjectives. Some people always use them, and others only when it's otherwise ambiguous or to group the words as a single idea. If you write "ten year old children" do you mean "ten children who are one year old" or "children who are ten years old"? It's clear if you write, respectively, "ten year-old children" and "ten-year-old children". But I can't see a similar ambiguity with "a ten page essay" (and note, I would use the word "page" thus.) Similarly for your first example, but in that case, I would probably write "with more than a quarter of its population of one million gone" to avoid the mental arithmetic you seem to be inviting the reader to perform.