I read somewhere it is not good to have it in a small refugium because it might be volatile in terms of it potential negative impact on water quality after it is full of waste.
plenum's are just as effective as methods of filtration. newer plenum methods include a piece of vinyl tubing that allows the under to be siphoned out on a less than regular basis (once a year?)
I have a close friend who still swears by the plenum and has had one with no ill effect for 7 yrs now.
FWIW, my advisor, Rob Toonen, conducted a study a few years ago looking at the effects of sand bed grain size, depth, and plenum vs. no plenum on aquarium water quality and organism survivorship. Including a plenum had no discernable effect compared to just using a sand bed. Sand bed depth had no effect on water quality for the measured parameters. Phosphate concentration was significantly lower with small grain sand as compared to large grain while calcium and alkalinity ended up slightly higher with small grain sand than large grain. Organism mortality tended to decrease as sand bed depth increased. He wrote this up for AAO, which you can see below: