I have never worked in a professional kitchen, but I have spent some time sort of observing how things work, primarily in very high-end Japanese kitchens in Kyoto, as well as reading and studying a lot about these things. And I've got knives of wildly varying quality.
My feeling is that BDL has 90% of the facts you need to know. What's missing has to do with the larger-scale everyday processes -- which he knows about too but hasn't mentioned.
If you're using good-quality professional knives, you need to emulate, within reasonable limits, the maintenance situation for which those knives have been developed. The American pro kitchen is something of a hybrid, weird place, but it's more like the old French kitchen than the Japanese. So if you use good Japanese carbon steel knives in the American kitchen, you have some work to do.
Basically high-grade carbon, properly treated, will not interfere with food. This is not a question of patina in any strong sense. High-end Japanese chefs polish their knives daily, including the ones used to cut onions, and when I say "polish" I mean gleaming shiny metal. The primary issue is to use excellent steel and a frighteningly sharp edge, and to wipe your knife with a slightly damp cloth constantly. Bear in mind, however, that slicing a case or two of onions at a stretch is an unusual task for this kind of kitchen, because the service structure is different.
High-grade Japanese carbon should be sharpened daily. I say this because this is how they are treated in high-end Japanese kitchens. This is part of the regular maintenance cycle, in other words. Different places work differently, but here's one common system. At the beginning of the day, chef starts sharpening the knives. (Yes, chef does it.) Because they are already very, very sharp by any reasonable standard, he does this on a very fine polishing stone, using always and only water. The knives are then wiped and racked, ready for use. (In a really big place, others help out with sharpening, but certainly the most important fish-slicing knives and such are going to be chef's province.) As the day continues, some knives may need to return to the stone. Whenever that happens, any bonded knives (kasumi style, with iron and steel bonded together) will temporarily produce just a slight off-taste, which comes from the ground soft iron interacting with the food; for this reason, some really high-end places insist on honyaki knives (which aren't bonded) for certain things in which that interaction is disastrous. Anyway, at the end of the day, the knives are polished, not on a stone but with polishing powder and the top slice of a daikon -- equivalent to the old French potato trick -- until they are completely shiny. The knives are wiped and put away.
If you're going to use knives like this in a kitchen that isn't structured this way, you're going to have to think about when you will sharpen and on what. Most western pro kitchens are not good environments for you standing there sharpening your own knives on your own stones. So you'll probably need to sharpen before you go to work or after you get off shift. Given what I hear about the rate of theft and abuse in these kitchens, I would suggest that you should carry your own knives to and from work, and do your sharpening at home -- the fine stones you'll need for the daily practice are not so cheap.
Now the question of using stainless instead is therefore really not about interaction with food. On the whole, all things being equal, which they never are, stainless is going to be harder to sharpen but will retain its edge longer. Basically it's more durable in both shine and edge. So the question is whether the stuff will stand up better, not to the abuse dished out by food, but to the abuse dished out by your kitchen and its denizens. Will a stainless knife survive better if the moron on the next station grabs it and cuts something on the stainless counter? Depends on the knife, of course, but first of all these knives are not so delicate as all that, carbon or stainless. Still, this is a worthwhile issue to think about in advance.
The abuse question also extends -- or is founded on, really -- you. Are you in a situation where you really can work very clean, wiping every time, constantly? Can you train yourself to do it automatically? There's no sin if you can't, or can't in this kitchen -- just buy excellent stainless and don't worry about it.
Anyway, some things to think about.