My theory....(Which is intuitively obvious in my opinion) Isshin is a member/ex member of the King's Royal Guard. This explains why other SS people don't know about him because they are all members of the court of pure souls who aren't even allowed inside parliment without an invitiation.
My guess is that Urahara and Yoroichi were not merely exiled but now serve the royal guard and were "exiled" in order to provide cover.
This also explaines why Isshin waited until recently to take out Grand Fisher. He could have presumably done this at any time since his wife's death. The fact that he waited until GF was Arrancar-ized says to me that he is acting according to a larger plan or someone's orders. (Many might think that as his powers were sealed by one of Urahara's Shinigami- to - human gigais, so he never even sensed the supernatural nature of his wife's death, the fact that he knew Kon for what he was based upon knowledge alone makes me think that he could make similar deductions about his wife's death.)