Beckett and Castle were greeted by Officer Hastings at the start of the episode, she's the one who removed the police line for them and briefed them. In fact she was framed right in the middle of the scene before moving to our left and out of the frame. You couldn't miss her. We were supposed to be distracted by all the other stuff and forget about her (which we did) but she was clearly there. Like Castle though I did not see the twist coming that she was the superhero.
As for the sword, didn't they mention that Lone Vengeance broke his blade when he attempted to slice the body? They also mentioned at the crime scene that he was sliced from the head on down to the crotch area, I assume while implausible that with a sharp enough blade and a skilled enough person who had experience cutting cartridge and bones (remember the killer turned out to be the butcher) that this would be possible.
I had no problem with the in episode plugging of the graphic novel, since it was first introduced last season. It's not like it hurt the overall plot and as pointed out it served to push forward the "Caskett" parallel in a fun way.
As mentioned earlier, I do like the fact that we find out that Beckett is a comic book fan and she geeked out at Castle's "Avengers #1".