I will raise the thread back from dead, because i have few things to add. First i will show the numbers i gathered from various settings.
- Aberrant has 1 nova per 1 million, which makes them lucky people who has a free ticket to fame and money.
- Paragons setting and Champions universe has 1 per 1 million ratio too. Though not all superhumans in those settings are as lucky as novas of Aberrant. It is also stated that only less than ten percent of them are bulletproof.
- GURPS International Super Teams have 1 metahuman born with powers per 100.000 baseline humans. In addition, 1 in every 10.000 people have potential to develop powers under certain conditions. This numbers seem good considering there are many teams of them.
- Extreme Earth setting has 500 metahumans per 1 million people, so there are few million of them but only around 1500 of them have potent powers.
- As stated in Wild Talents book, Godlike setting offers 1 talent per 10.000 people, makes them more common and down to earth.
- In Reckoners universe of Brandon Sanderson, it is stated in first book that there are few thousand epics in post-apocalyptic version of Chicago, only few dozens of them are invulnerable to conventional harm. It is hard to deduce a ratio from post-apocalyptic setting because population of Newcago wouldn't be equal to modern Chicago. I assume there are 500.000 people in Newcago and 2.500 epics of which 50 of them are invulnerable, which would give us 1/200 ratio of epics and 1/10.000 ratio of high epics.
- Marvel mutants seem to be in millions but i don't know an exact ratio. It might be around 1 mutant per 1000 people or even more.
Gurps Supers book give some guidelines to number of supers. If you want to have team of supers in every big city 1 per 200.000 people is suggested. If you want a superteam for every big town 1/10.000 ratio is offered.
As Ares stated, this ratio is dependent of their power levels and function in the setting. I can see two main camps along that lines.
First is an everyday people with mostly useless or low-level powers scenario. Stories in which poor mutants hunted down by government or far-right voters would fit that bill. X-Men is the trope maker on this, TV shows like Heroes, Gifted, Alphas are also good examples. I would say 1/10.000 would be a good base for that goal. We would get few hundred metahumans in big cities and roughly 800.000 mutants in the world. This ratio could be increased of course but i personally would not go above 1/1000.
Second scenario is that most metahumans have powers strong enough to enable them to be superheroes or dangerous mercenaries, elite government agents etc. 1 or 2 superhuman per 1 million population could be enough for that. That would give 300-600 supers in USA, 80-160 in Germany, 1400-2800 in China and 8.000-16.000 in the world. In Aberrant where each superhuman can become a celebrity or in Paragons which some supers offer themselves as gods this makes sense. 1 in 250.000 or 200.000 would be better if those powers are hereditary and there are metahuman families in each big city.
I'm not sure about 1/100.000 ratio. It could be good for a world where most superhumans have useful but not exactly superhero level powers, like in the movie Push or Heroes series. Also it might be proper for a game in which powerful supers are more common and integrated into society as soldiers, policemen, entertainers etc or if you want few superhero or supervillain teams in every big city.
I excluded badass normal or power armor types from this projections and mainly thought about mutant-like origins. Also i used base populations of big cities but they would more likely attract few times more superhumans than other settlements.