I'll try to answer a few of your questions. Yes you are circulating the same water, but that's exactly what you're doing all the time with any water movement scenario in aquariums. What else would you be doing? It's the movement of the water that is required by sessile invertibrates.

Small animals from the refugium sometimes do get killed by pump impellers; how much is not really known or agreed upon. Larger pumps tend to have more clearance within the impeller, and are thought to be less lethal to small animals. But, most of the animals that get swept into the water stream are VERY small, microscopic larvae, etc. Larger animals like adult amphipods and mysid shrimp are usually good enough swimmers to stay out of the return pump.

You have a lot of hermits; these will also decimate your copepod population in a small tank. I'm pretty sure the only way you'd have success with a mandarin in this size tank is to find one that wil accept food like frozen bloodworms. They definitely exist; you just have to find one. I had one in my 10 gal for over a year. Ironically, when I moved it to a larger tank, it got swept up in the overflow and died.

HTH