Some of them may have some suspicions, but they don't seem to really know. As pointed out in the comments, Theon is supposed to know Arya, so Bolton uses him as a witness to confirm Jeyne as Arya:
Theon Greyjoy had grown up with Arya Stark. Theon would have known an imposter. If he was seen to accept Bolton's feigned girl as Arya, the northern lords who had gathered to witness the match would have no grounds to question her legitimacy. Stout and Slate, Whoresbane Umber, the quarrelsome Ryswells, Hornwood mens and Cerwyn cousins, fat Lord Wyman Manderly... Not one of them had known Ned Stark's daughters half so well as he. And if a few entertained private doubts, surely they would be wise enough to keep those misgivings to themselves.
They are using me to cloak their deception, putting mine own face on their lie. That was why Roose Bolton had clothed him as a lord again, to play his part on this mummer's farce.
(A Dance with Dragons, The Prince of Winterfell, pages 533-534, Bantam Books Mass Market International Edition)
Lady Barbrey might know about it, as she is one of the only one to truly support Bolton. But even her case is unclear. And Wyman Manderly seems to believe Jeyne is the real Arya, as the wedding is one of the reasons why he wants Davos to look for Rickon:
"Roose Bolton has Lord Eddard's daughter. To thwart him White Harbor must have Ned's son... and the direwolf."
(A Dance with Dragons, Davos, page 433, Bantam Books Mass Market International Edition)
Also remember that Jon sent Mance to get her because he thought it was Arya, and even when receiving Ramsay's letter he still thinks it's her. I think the northern lords who join Stannis also mention saving Arya as part of their motivations, though I can't find a reference for that right now.