No worries on the sponge filter. There's no impeller, so no chopping up. If any shrimp get in the holes when you take off a sponge, when yo put it back on- the current carries them out the top. I personally have almost no worries about it, so I even remove the extension tube on my double sponge filters. I like the way the bubbles spread wider without it.
When I take off the sponge, I roll it like a log in the tank and any shrimp on it come off before I take it out to squeeze..
My suggestion is to only clean one sponge and let at least a week between cleaning the other. This way the bacteria is still on at least one if accidentally squeezing out too much bacteria on the other. By waiting to do the other one, you also allow bacteria to start recolonizing on the "clean" one. In short, it is entirely possible to crash a tank by squeezing both out at the same time. yeah...it's happened to me.