Shioda mentioned at times that Ueshiba's Nikyo didn't hurt - rather, it unhinged the knees. I think that the Yoshinkan tends to follow this method (if they can), which fits in with the OP's experience (at least, that was my experience with the Yoshinkan).
Thanks. What are your sources for Shioda anecdotes? They are definitely teaching a non-painful nikajo here in Kyoto, but sometimes it degrades into painful nikajo. Especially during hajime geiko.