If the game keeps having spikes the whole time, it's probably not loading that's causing the problem so it doesn't really matter if you use json or binary. I recommend json for Nate's reason and for diff tracking.
I've easily had 30 animating spine skeletons before and it wasn't hiccuping.
But as you need more and more skeletons, you'll want to make sure each individual setup is not being wasteful.
In general, be judicious about the little details you add to your multiple-spawned skeletons. When there's a lot of them, your tiny separations and animation details possibly won't even be noticeable and only hurt framerates.
This ONLY applies to skeletons you need to spawn a lot. If it's just one skeleton like your main character, the effects can be arguably insignificant:
(1) Minimize the number of keyed properties in spine. For example: If a bone doesn't need to rotate, don't give it a key to rotate. Anywhere. That item shouldn't have a row in the dopesheet. Each row in the dopesheet is extra overhead. So even if you only have 1 key on it, it'll eat up resources. (Each dopesheet row is one Timeline runtime object that the runtime has to iterate over every Update an animation makes.)
(2) Have as few bones and attachments as possible.
(3) If you can help it, don't use meshes and FFD. And if you really need meshes for these skeletons, minimize their vertex count.
(4) If your skeletons are for looping environment stuff, and you want want it to play one animation over and over, Baking may be a good option, especially if you just want it to do a Weighted/Skinned animation. Baking will take advantage of the GPU to animate the meshes and free up your CPU to do the more controlled things. For maximum compatibility with Unity GPU skinning settings, make sure each VERTEX is bound to a maxmimum of two bones.
In this context, it'd be informative if we could see what you skeleton looks like.
You can replace all the images with pink boxes if you want. Or show a wireframe of them in Unity.
I was just speculating. Your skeleton setup could be fine. But with only 30 skeletons in your game, what else could it be?