I think it's better to include the honorifics, and the users above already put pretty good examples of why. Also ppl know they areding/watching manga/anime and that it comes from Japan and so it will have some things that cannot be translated and have to be included to get a better understanding of the scene or the character's personality...
But, @brycec, I think it would be better if you tell us what was the part that looked awkward in that manga translation, bc otherwise, I can't think clearly of a example when honorifics are awkward...I imagine it's something related to the story or a scene not being set in Japan?