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I don't think shades can reproduce. The just don't age.
Here's the short explanation, and I'll admit beforehand that I might have some details wrong because it's been a while since I read it:
Gestalts (souls) are immortal, but replicants (their bodies) are not. For the last 1300 years, Devola & Popola have been making clones of replicants to replace the old ones while they wait for it to be safe to combine bodies & souls again. At some point during that time span, the replicants began to speak and develop consciousnesses, and they even built their own villages. Despite being intelligent, they can't reproduce because they don't have souls. Gestalts can't have children because they don't have bodies; the smaller shades you see are simply the souls of children.
Gestalts that are separated from their body for too long begin to break down and go insane. A gestalt breaking down is also what causes the black scrawl to appear on its associated replicant. Most of the shades you fight in the game are gestalts that have lost their sentience, although some are not. The non-aggressive shades you fight near the beginning of the game are just children that don't have any reason to fight you.
There are some gestalts who, when they realize what is happening, try to stop it by forcefully combining with a replicant that isn't their own. This is what happened at the Aerie; a lot of the people there are gestalts possessing replicants who are afraid to go outside because they're scared of the sun. The gestalt and the replicant's consciousness fight for control of the body and eventually go insane. When the replicant eventually dies, or if they fail to combine, the gestalt emerges again, making it look like the replicant "turned into" a shade.
I don't recall if Grimoire Nier specifically says what happened at the Aerie, but the impression I always got was that the gestalts there knew Nier was going around murdering shades and they were expecting him to come for them, so they set a trap to kill him.
The Replicants are recreated roughly every century. Each batch is overseen by the observer androids (like Devola and Popola) as they await the death of white chlorination. So the current Replicant Nier and Yonah are not the first ones to exist.