They were, actually. Many were, at least. For example, vault 87 tested the creation of super humans (which became super mutants, and is the breeding ground of them). Many of the vaults were used to test drugs and for psychological experiments.
I go off Interplays cannon to me, only the Mariposa Army base had large vats of FEV. People were dipped into large vats of goo then sent then put into confinement where they would change. There were lots of dumb dumbs like Harry, but there were plenty of smart ones like Marcus and the Lieutenant. In fact the most indoctrinated and intelligent mutants are the nightkin were the smartest of super mutants.
There was vault 12 which was made to demonstrate how the vaults would work, but the door never properly shut. So it's population either died or became ghouls.
Then you had Vault 15 which was only meant to stay closed for 50 years then open. This caused panic and the surviving populations broke off into several groups. Three of them became raiders known as the Khans, the Jackals, and the Vipers. The last formed an Arab themed community called shady sands.
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