I currently have over 100 regular arrows after purchasing them from the stores. I've now waited until after a Bloodmoon and the arrows still have not respawned in shops. I've tried purchasing other items and they seem to respawn fairly quickly, but not arrows.
Arrows will only respawn in shops if you have less than 50 arrows of that type (e.g. Normal, Fire, Bomb, etc).
As such, the best method to stock up on arrows from shops is to use up arrows until you have 49, then buy arrows from all the shops at once.
The only exception to this is Ancient Arrows
These will always be purchasable from Cherry at the Akkala Tech Lab
Teleport to all the stables you know about and talk to Beedle in front of each one. I did that for the 12 or so stables I know about, and I had >200 arrows by the time I was done. He was still willing to sell me more as I found him in new locations, but I had enough and didn't buy at that point. I'm sure he restocks during a blood moon, but you can get far more from him at the various stables than you can at the shops in all of the cities.