I can think of a simple reason why Nintendo likely cannot detect headers beyond looking for dupes or perhaps gathering large samples of logs to check if the same header is used on multiple different games: if they could tell simply by looking at the header, they would refuse to let the game online entirely. It doesn't make sense to let pirates join in, even for a little while, and then ban them later. A banned console cannot play online, whereas a headerless game can't play online anyway, nor could one with a detectable fake header. Given that the end result is always the same, it wouldn't make sense for Nintendo to willfully let them online, even for a little while. They already have some entry-point checks in place that immediately refuse access to consoles with no headers, why not just put the ban code there? They likely don't know so they have to wait long enough to see multiple copies of the same header, then they ban.
If that's true there still remain to be seen if they can also tell when the same header is used on multiple games, or, indeed, if they've started keeping better track of headers on more recent titles, and more easily banning on those.
