NPC's from "Base" has disappeared.

[Oscar One]

Gradually, as I progress through the game, some of the NPC vendors have disappeared from the Base, and some important items are bought from these vendors... only Pieta and the Woman in the blacksmith's shop are here. Is this normal? Are they somewhere else?

[Khryst]

the executor moved down the stairs to the hallway to your left if facing the vestige.
as for the others, yes it's normal for them to move as they have questlines that you interact with them.

Some NPCs you meet in the world will also "move in" as well, and some will "move out" as you progess and their storylines progress too.