It is true that in the Iwama weapons system the bokken is generally considered to be a striking weapon. Do you have a reason to believe that at some point, the founder held a different view (say, that the bokken is just an approximation if a shinken) and the change of shape reflects a change in the attitude?
Haven't really reflected much on this, but my understanding is that Ueshiba studied actual sword arts albeit in short stints, not mastering any one in particular but absorbing and changing things (in aiki we do it this way...) as he learned them. Despite his take of martial movement with weapons, I have very little reason to believe he treated his aikiken -- technically -- as anything other than... a katana. Did any of the ryu-ha he studied treat the sword as a hitting instrument, and did he treat it that way at some point in his aikido development? Maybe, but I just don't see it. As for change of shape and attitude carrying to today, it wouldn't surprise me as it's not uncommon for somebody to start something and for generations to copy it down to the little mannerisms without ever questioning or thinking. But I leave the question of if/when/how to the historians.