Ammo supply behavior is a bit quirky, especially when it comes to resupplying.
Setting a "x" amount of bolts for hunting in the supplies screen defines only the sum total of bolts that your hunters will have access to at any given time. Each hunter will then try to fill their quiver as best as they can. The quivers themselves have a limit on how many bolts they can hold so that's why the dwarves only carry 25* at a time.
And then we come to the actual hunting, which has it's own set of quirks. You could have set everything correctly but your hunter might just want to do something else. I have had forts where the hunters were mercilessly hunting every wild animal in the map and others where they were doing nothing but standing in the tavern. Giving the hunting labor to a different dwarf fixes this sometimes.
I've also noticed that hunters tend to not hunt flying creatures. Probably due to pathfinding. That means that for whatever length of time your map has only fliers the hunter will be doing nothing. Coupled with the fact that in most embarks there is nothing but the player to hunt down those fliers that results in them staying in the map far longer than ground animal, preventing any new animal to spawn and further extending your hunters idle time.
If your dwarves are desperate for food, the easiest workaround is to use a military squad (either melee or ranged works, but ranged can also attack fliers) to manually hunt. Your civilians will butcher any animal you kill that way just like if it was killed by a hunter.
*There are some tricks to get more than 25 bolts. The highest I have seen is 49 if I remember correctly. This can be achieved by assigning enough ammo for each dwarf in the squad to have 50 bolts. They will then equip themselves with a stack of 25 bolts and when they use some of them they will eventually equip another stack of 25.