Because there are so many humans that someone’s almost definitely gonna have it. If there were like a million people, then we probably wouldn’t see many of these traits, but there are 8 billion people around. That means on average, traits that are one in a million are in 8,000 people. Traits that are one in a billion are still likely to be in a handful of people.
If it’s incompatible with life, no one will have that trait, because no one will be born with it. If it merely prevents you from reproducing, it just won’t be heritable, but the mutations/anomalies will still happen, so people will have them.
Sure, but your original question was about evolution getting rid of the genes necessary for a micropenis. That condition is very possible in our gene pool. Yes, there probably aren’t people who grow fins, even though that’s technically possible with enough specific mutations, so sure, evolution will eventually effectively get rid of traits in a species even if they’re not life threatening (though enough mutation for a human to grow fins would probably be deadly), but then your talking about evolution on the scale of millions of years.