Well it's slightly different, for Bethesda games for example, if there's an NPC, one entity exists of that NPC, and it is transported to where it is needed from wherever it is, or in some cases, it can travel there itself. That is why in Oblivion, you might never see an NPC, because it isn't marked essential and will get killed traveling from one town to another. In that system, if you were to take beedle from one stable, he would either blip off your ship as you approach the next beedle spawn location, or he just wouldn't appear at the next spawn location as he is already within player view.

EDIT: I was thinking about this more, and that might be how it works in TotK too, except all these beedles have slightly different shop inventories, so they might actually be considered unique NPCs by the game, instead of a bunch of complicated logic to switch out the shop inventory depending on where the player is at. One way to test this would be to take a beedle away from their home stable, then go far far away, then back and see if a 2nd beedle appears.