I don't think Daito ryu has had any influence on okinawan fighting methods. IF (and that really is quite a big if) there was any kenjutsu influence on some early karate, then I would look more in the direction of the Satsuma clan tradition, which was Jigen ryu. There have been some speculation that some karate great, I think it was Bushi Matsumura, was also a master of Jigen ryu, but I don't think that has been confirmed by any actual research.
I did not mean that all samurai would be students of Daito ryu, only that they would practice something that looked a lot like it. The Takeda clan and the Daito ryu were one of the major ryu, however, dating back to the Minamoto.
Right, these are both in line with the general picture I was suggesting—it wouldn't have to be Daito-ryu Aiki specifically; the crucial point is, it would be some (ryu-specific?) empty-hand adaptation of the kenjutsu techs (of that ryu) which—this is the important part, I think—will look quite different, apart from isolated parallels, from modern karate in any of its local flowerings. And yes, it is a big if, although I think Abernethy makes a reasonable case for it.