Certainly a lot to think about. I think in the short run (next 5-10 years), there will be some loss to attendance in certain dojos. Aikido has a reputation and people come to train with that reputation in mind. If they walk in and find people not training in what they had preconceptions of, then they won't stay. I have personally experienced that ... several times.
But, in the long run, I think maybe attendance will pick up ... because the perception and reputation of aikido will have changed. This is where I think one of two things will happen (here in the U.S. No clue what will happen in the rest of the world).
1. There will be a split (not necessarily anti, or against each other, but just two different camps). One side will hold to the current perception of Aikido and have students training in that. And the other camp where IT (Internal Training) and aiki have been reintroduced. I think the former will be more well known and have more overall dojos than the latter.
Why? IT training is not for everyone (not that everyone couldn't do it, they can. But that the amount of solo training and the mind-numbing repetitive, mentally exhausting work will not appeal to many). Regular Aikido has an organizational structure that will appeal to the masses. Training has been systematized for the masses.
2. This IT will overtake and overcome regular aikido, causing a shift in perception of the martial and spiritual viability of aikido. People will find a way to merge systematized aikido training with IT. Americans will emerge as leaders of organizations and they will have aiki as seen in Shioda, Tomiki, Shirata, etc, and maybe even Ueshiba or Takeda. A shift in *who* trains in aikido will most likely occur, also. You won't have as many people looking for "harmony". I think the "spiritual" nature of aikido will still be there, but not in its current incarnation.
Really, I think in the long run of 20 years or more, option 2 is going to happen. Once people get enough IT (10-15 years) and get out and about, a lot of the people they meet will want what they have. And I think there's going to be a myriad of Internally Trained people -- just like there's a difference between Tomiki's usage and Shioda's usage and Shirata's and Ueshiba's and Tohei's, etc. Some will have more "power" and some will be softer (but yet powerful). Skill levels will all be different. But, between then and now ... ack ... as you stated, change is not always liked.
One of the interesting questions is What is Japan going to do?