I checked the source briefly, and the problem is that the source draws every single rectangle manually every single tick. That's very inefficient. Just draw a rectangle to a Texture once, and create a bunch of sprites using that Texture. Pixi should be able to handle at least 10x the amount of rectangles if you do this.
https://www.goodboydigital.com/pixijs/bunnymark/
I checked the source briefly, and the problem is that the source draws every single rectangle manually every single tick. That's very inefficient. Just draw a rectangle to a Texture once, and create a bunch of sprites using that Texture. Pixi should be able to handle at least 10x the amount of rectangles if you do this.