the pdf format can embed various other formats bringing a sort of interactivity to pdf documents : u3d, prc, flash scripts among others. From various sources online, it looks like the flash format is slowly coming to an end because of the rise of the html5 protocol for the construction of sophisticated webpages. In case of the disappearance of flash, will the pdf format be updated to incorporate a new type of interactivity? Predicting the evolution of the pdf format on that specific aspect of interactivity and virtuality seems quite arduous.
You can only really get speculation here at best on that but HTML5 is not replacing Flash. They're used for entirely different purposes when they're used in a best practice manner. Besides, Adobe has full control over PDF, Reader and Flash. I see no reason they'd remove support for their own products from, well, their own product.
If it's not already there in newer Acrobats, you may see a HTML view pop up, which would just be an instance of the OS's embeddable browser. Something very easy to do.
I agree that we are dealing with speculation here but it is not rare to see companies abandon a product because its maintenance/development becomes prohibitely expensive.