Refugiums should'nt cause bacteria problems if done properly (adequate flow, shallow sand bed, as well as keeping HARDY macro algea such as gracilaria, caulerpa, and cheatomorpha). I prefer a shallow sand bed to a deep sand bed simply because I am not comfortable taking the risk of accidently releasing sulfer and anerobic bacteria in the water column from a DSB. Yes I know a DSB has its advantages, but its not for me. The refugium provides a safe breeding ground for copepods to replenish the DT. If a refugium still cannot keep up with gluttonous fish a culture tank is your surefire method.
To answer your question about the benefits of amphipods. Yes they are beneficial as a food source. Amphipods, copepods, rotifers, krill, and mysis are all zooplankton. The ocean food chain is as such: phytoplankton is eaten by zooplankton, which is eaten by fish.
The culture tank can be small 5-10 gallons. So space is very minimal and can be kept really anywhere, even a garage. In a peer reviewed article by Doctors Zaleha and Busra they successfully bred copepods in water between 40-110 degrees but had the highest yield in around 78 degrees and a salinity between 5 and 25 parts per thousand. So temperature and salinity are not too big of a concern if you ask me.
If you decide to give it a try you should do bi-monthly harvesting and weekly phyto dosing (enough to have a medium green color. If the water turns clear then they consumed all the phyto). You'll need a cheap refugium light to keep the phyto alive and a very small airstone or bubbler running slow enough that you can barly count the bubbles. The phyto dosing keeps phosphates out of the DT and drastically speeds up breeding. Finding a way to keep your temperature up will speed up both breedy and sexual maturation, but is not necessary. Pretty simple if you ask me. Not to mention that its a healthy natural feeding method in contrast to processed foods.
For benthic copepods a standard 5-10 gallon tank is great due to the larger surface area along the bottom of the tank for them to breed. If you want pelagic copepods (water column types) a five gallon bucket works better because it is tall with a larger water column for them to swim in and reproduce. Pelagic copepods would be beneficial if you keep anthias, seahoarses, etc.
Happy reefing