I would be lying if I said I knew the best way to filter a reef aquarium. The delicate balance between nutrient import and export, and bacterial assimilation (nitrification) and dissimilation (denitrification) is the true challenge of the hobby.
We know that our captive reefs have a surplus of trace elements (heavy metals). These can be removed chemically or mechanically, as they are usually attached to detritus (POC), so in many ways a mechanical filter is a chemical filter. A significant amount of bacteria is attached to detritus, both in the substrate and free-floating in the water column. Protein skimmers and filter socks remove POC, bacteria, calcium, zooplankton, and heavy metals. Some of these elements are "good" and some are "bad". The good stuff is easily replaced with nutrient import (feeding).
My conclusion is... feed well, filter "weller". As long as you maintain adequate marine snow in the water, the corals and fish will thrive and with a collection of seemingly superfluous filtering devices, you can remove residual Po4 (phosphate) & No3 (nitrate).
There is no shortage of filtration options, some more valuable than others. You must weigh the initial cost, operational cost, maintenance, convenience and residual to measure their merit. I find filter socks to be cheap and easy with little residual if you have the time to clean them at least twice a week. The bacteria removed by skimming are only the free-floating "castaways" from the exponentially larger colony of bacteria in the substrate so lower bacteria rates in the water column doesn't bother me. Sponges primarily consume bacteria so a benthic/cryptic zone would lower bacterial counts, and a skimmer limits the growth of sponges.
Bacteria is easily fostered with the addition of a carbon source such as vodka, vinegar, glucose or biodegradable polymers. In my opinion, the carbon source should be added directly to an anaerobic bacterial bed, rather than poured randomly into the water column. The danger with low nutrient systems is you deprive corals of inorganic (dissolved) nutrients. You must compensate for low inorganic nutrients by increasing organic nutrients. A partially automated system that slowly adds zooplankton and phytoplankton will make up for our mini waste water purification plants.
I have had good success with non-hatching decapsulated brine shrimp eggs, finely ground plankton, and frozen cyclops. Some people swear by oyster eggs, but I can't justify the cost.