Glad you already found reasonable performance, even before doing all the easy optimizations (eg prune).
Clipping can be used, it just has a cost. There's a big different between clipping a handful of triangles using a 3 vertex clipping attachment and clipping 500+ triangles with 13 clipping attachments. 🙂
Deform is similar. It's absolutely fine to use when needed, but it's wasteful if overused and often can be avoided by using weights.
Everything has a cost, it's just a matter of staying under the threshold where the sum of all the costs become too much. Spine doesn't try to force you to be efficient, so it's good to figure out how to keep things reasonable before having created tons of rigging and animation that may need to be adjusted.
For the most part it's pretty straightforward: use fewer bones and vertex transforms and be wary of clipping and deform keys. Often you can use weights where at first it might seem like bones are needed. Like these tips:
The 5 cream toppings use only weights, no bone for each one.
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A single bone for a faux 3D cube.
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More tips here:
http://esotericsoftware.com/spine-tips