Shells Are Clothes
So, shells in the Mario world are not necessarily biological but more like a type of clothing and possibly power up with variations of a single shell.
While not everyone remembers this but Koopas quite often could be kicked out of shells and run around without one Super Mario Bros. 4 Super Mario World, Super Mario 3D Land, Super Mario 64, etc. Even in the original Mario Bros. the Shell Creepers exit their shells to flip it. In Paper Mario 64 the Koopas of Koopa Village have their shells stolen by Fuzzies, one Koopa mentions their shell is custom made, this shows them to be something that can be ordered and worn.
This is further shown with characters like Bowser in the RPG games switching out shells, and Mario using the Blue Shell power up. Mario uses a Blue Shell Power up and block in NSMBDS and M&LBIS. There is also the Lazy Shell from SMRPG.
Not to mention Mario and Friends in Super Mario 3D World can enter empty Koopa shells.
They also seem to serve as power ups themselves Bowser gaining abilities from different shells, certain shells in SMB4SMW being able to chase Mario down when piloted by a Kamikaze Koopa, or even how when a Yoshi eats the SMW shells he can spit fire or grow wings.
We also see Blue Electrokoopas remove their shells and send it flying at Mario as a form of attack.
The shells are probably made by a company that is connected to the Strike Equipment from Mario Kart who Mario Red, Green, Bowser, and Spiny shells for kart races.
We also see shells being worn by non Koopa creatures as well that don't normally need shells like Goombas, Konkadors, and Ant Troopers. Yoshis themselves could be a Koopa as mentioned in a previous post, and like Koopas they are born without their shells.
Some shells might even be extra heavy causing Koopas to go on all 4. Written by Eris the Lorekeeper