I think it's important to think about the audience a bit. In an academic translation, sure, go nuts with long footnotes. But I think in the case of something intended primarily to entertain people you should make some concessions to practicality. Even many fansubs just swap in some English pun to go for the same effect (which leads to kind of funny results like fans who watched the fansubs complaining the dub "changed the original dialogue" from something that was also not the original dialogue).
But while some people have no problem with "adapted references" other people have.
And I disagree with you dismissing it as "just entertainment". It is clearly very important to some people. It should be respected and cared for for the sake of not only the fans but it's creators as well.
I suppose what I meant to say is that being entertaining and giving painstaking analysis of every pun are goals that are sort of at odds with each other.
