Don't copy. That's the golden rule. Buy a book if you want (as there are now Super Mario and Zelda books out now as well) but if you're arranging, don't use any elements from the book. Nothing. For that reason, I would actually advise against buying any books if you arrange, since the temptation won't exist. Essentially just act like you don't have access to the book and you're good.
Regarding quality, just do your best, keeping in mind what I mentioned before. I have seen things in official books that I would either change or consider altering if I was in some kind of editing position there (as I am here). Not all (even official) arrangements/sheets are flawless.
but I have a hunch that commercially available sheet music gets in the way of (our) fan transcriptions in more cases.
Not sure what you mean by this.
How does commercially available video game sheet music affect the rate we submit transcriptions for that game
Not sure what you mean by this either.
Maybe I was totally off with regards to your question and if so, apologies. These are my thoughts on the subject in general.
There are advantages (from a consumer's standpoint) to purchasing official scores over free alternatives such as ours. Most practical being a guaranteed accuracy with regard to essentially every element of the score, clearest intent with regards to any text direction within, and (everyone's favorite) the far-nicer aesthetics including but not limited to images of the copyright-protected mascots plastered all over the book/score (even it being a book is fancier). So I don't think that what we do here is a significant detriment to the selling of the official scores, but as a disclaimer, be aware that I have no facts to back up that statement. However, based on what I've also noticed (primarily regarding the aforementioned Super Mario and Zelda books), Nintendo (in this instance) doesn't seem very concerned with these official scores. I say this because rarely do we get even soundtracks from Nintendo (which would not only sell better but also appeal to a much, much greater market). This seems to suggest that Nintendo isn't counting on making tons of revenue from these scores. Another thing I've noticed (again, this applies only to the Mario and Zelda books) is that one single person is responsible for all the arrangements. And I mean the same person for both series. Not to say this is what happened, but it wouldn't surprise me if (perhaps this very person) wanted to arrange scores (much like we do) and so pitched the whole "official score" idea to Nintendo, and they saw some decent credentials and said "Sure." The whole thing just kinda lacks support from Nintendo from what I see which is kinda unusual and doesn't make sense for things that they really bank on. Nintendo is careful and they are very vigilant.
*I'm gonna try to use very careful language for this next part; because this is the internet after all*
If my conclusions are correct therefore, it likely just is that Nintendo isn't as concerned about the official score line to justify them going to great measures to enforce the whole score thing. That would explain why we haven't had problems, despite the possibilities you have suggested. Unless we've somehow existed underneath Nintendo's radar this entire time (which I can almost guarantee is not the case (heck, we've had Chad York on the forums with us)) it seems like a rather chill relationship where as long as we don't charge anything for our services and stay out of their way, they may see fit to just leave us alone. It's a relationship I can definitely live with.