Well, random noise hides it if the random noise is higher. That's why you don't see the line-banding in shadows on some other brands of DSLRs that use CCDs, at higher ISOs; they have more random 2D noise, which hides the patterned noises. If you actually extract a map of the banding offsets, however, the CCD cameras can actually have stronger banding.
Certainly many should be implemented as an option. There is no point in a converter wasting CPU cycles looking for unequal amplification patterns on a camera that doesn't show them, or in shots where they don't matter, but it is actually a very simple process. All the converter really has to do is sample the average green value for each line, and detect a pattern, and then scale the values in the lines (red and blue, too), preferably at a higher bit depth (or the depth is already deeper than necessary, as seems to be the case with the 1DmkIII). The value in being able to turn a feature like that off is that you may have taken an almost perfectly regristrated exposure of actual lines, and the feature would weaken them. Even with the slightest angle, however, the lines should be safe.
There may be some amplifier sag in that "portrait.jpg" camera; it's hard to tell without seeing the RAW. That would probably require some profiling, to see how the amplifier reacts to a real B/W edge, and base corrections upon it. ANd really, if you want maximum quality from any camera's RAW files, the converter should know all of its repeatable flaws. The converter could ask you to take several shots of a smooth wall or card, completely out of focus, and use their common artifacts for a flat-field adjustment. It could ask you to take a sharp shot of a big black square on a white background, to see if the amplifiers sag. Individual errant pixels could have their unique sensitivities mapped, etc, etc.
I find it rather sad that almost all post-processing of RAW shots is after conversion. Artifacts are so much more distinct in the RAW state; waiting until after conversion to remove them is like dropping a chocolate bar into a pot of soup, and instead of just removing the chocolate as quickly as possible, letting it melt and stirring it in.
If I could run something like Filtermeister from ACR, and run it on the RAW data just after decompression, I'd be a very happy camper.
