No they're not frowned upon, but some people feel they have some downfalls. Many believe they can be a nitrate factory with time, but others use nothing but wet/dry's.
The sump/refugium seems to be the most popular option which is not too different as far as plumbing setup is concerned.
You've probably read this, but in case it gives you more info... A sump will increase your total system volume and give you a place to hide all your unsightly gear like skimmers, heaters, carbon filter, probes, thermometer etc. Depending how large your sump is, and how its setup, you can do all your waterchanges in it and never adjust the water level in the main tank, therfore keeping it undisturbed.
Adding a refugium can be a separate small tank or just a compartment within the sump itself, but the latter requires lowering the flow rate to ensure the refugium goes undisturbed.
Refugiums work well at nutrient removal because essentially, the macroalgae within the "fuge," utilises the waste products to grow.
any of these require a overflow if you don't drill your tank.