I'm busy with the Hype book project, so I was only able to look at the project briefly. It looks like your particles are using the "Dynamic" physics setting. That's basically a heavy element. It's using a lot of physics processing. Typically, particles are light-weight actors, so that they don't slow down.
Basically, it looks like there are too many heavy actors.
I'm not sure what you could do to easily fix this problem. It's why I've been posting so much on the Physics API thread. Hype is really close to game development software, but it needs to tap into the matter.js API.