If so many things are not easy to implement it worries me as that would indicate that the coding is quite messy in structure.
This sounds very much like a statement from someone who has never worked on commercial websites (maybe you have, in which case you should know better). Frankly, almost *nothing* is easy to implement when you have to deal with large databases with scaling issues being accessed by users all over the world using all sorts of browsers in many different languages.
That said, even a cursory look at the NT pages should give you a hint at why this might not be trivial to implement: NT ID's are not part of the regular team ID sections, NT overview pages are NOT identical to club team overview pages, the relationship between team ID and manager is not static (nor is it for club teams, but it's dynamic in a totally different way), enthusiasm changes are calculated differently for the NT than for club teams suggesting GE differences, league/playoff structures are totally different, and on and on and on. Any one of those could make it difficult to implement, the combination of all of them (and more) certainly means it's likely not going to be a cut-and-paste job from the code for club-based trophies.
On top of all of that, if we know anything about how the BB's operate, when they put this in, they will want it to be an automated process that will work in the future with whatever other changes they might be planning. So a one-time manual assignment of trophies to the winners is not likely to be a solution they find appealing.