For the last week I haven't been able to get more than one Fairy to spawn at fountains. It seems the game thinks I already have fairies in my inventory, but I don't. I'm trying to stock up to make fighting the Thunderblight Ganon a little easier.
I read on some post somewhere (I apologize, I can't find the post. If I can find the post again I'll edit my answer to include a link) that sometimes if you have been playing your system for a long time without actually turning it off (really off, not just sleep mode) then some things, including fairies, won't respawn after the blood moons. Try saving your game, turning off the switch, and then turning on the switch again and then playing the game again (you may still have to wait for a blood moon though).
If you are looking to maximize the number of fairies you have, there are tricks (see this link which refers you to this link for example) in order to get 11 in your bag. Edit: The trick basically is to collect 3 fairies from the first fountain, then go towards the second fountain but before you get to the area hold 2 fairies so you only have 1 in your bag (which should allow 4 fairies to spawn, under normal game mechanics) and then put away the fairies you're holding and collect the 4 fairies that spawned, then go to the third fairy fountain but before you get there hold 5 fairies so you only have 2 in your bag (which should allow 4 fairies to spawn, under normal game mechanics) and then put away your fairies and collect the 4 fairies that spawned. This should bring your total to 11 fairies.