I understand your concerns (I truly have the same concerns) but, unfortunately, I have no more insight into the future of AIR than you do and, at this moment in time, I genuinely have no news on the future of JuiceboxBuilder.
All I know is that Juicebox itself is still alive and that work has started on the next version (which will likely be a bugfix release).
I really do not know any more than that. I'm sure that the developers are aware of the AIR issues and all we can do, myself included, is hope that JuiceboxBuilder can live on in some form or other beyond the Harman procurement of AIR.
I wish I had more information (good or bad) to give you but I'm as much in the dark as you are just now.

It should be noted that there are alternative ways of creating Juicebox galleries that do not rely on JuiceboxBuilder and AIR. I realise that these methods may not be suitable for all users (and it is certainly a less than ideal scenario) but the Lightroom plugin at least provides Lightroom users with a longer-term solution (with the Pro version of the plugin featuring full control over all Pro configuration options just like JuiceboxBuilder-Pro).

I'm sorry that I do not have any more information at this time but I'll be sure to post back here if I hear anything relevant to this matter.
Thank you for your concern and continued support of Juicebox.