In theory yes, but with caveats.
The way that rich media (video/audio/3D/SWF) is embedded into a PDF is defined within Adobe's extension of the ISO standard, and that takes years to change; you're not going to see a sudden change to HTML5 embedding just because Adobe killed Flash. But since with embedded audio and video rich media the actual content is always stored in a format that can be read without using Flash (e.g. videos in MP4, audio in MP3), a PDF viewer doesn't need to involve Flash to play them. As it currently stands the "player" is also embedded, e.g. for video it's a tiny SWF file called videoPlayer.swf - and Acrobat in turn loads that into its own copy of the Flash runtime. But it doesn't have to - it could simply read the content and play it through a native widget, just like Web browsers do. The decision to cobble together the Flash playback system was partly to promote Adobe's own software by preventing third parties from implementing all the features in Acrobat, and partly to get around the hassles of the legacy media annotations, which relied on popping open a compatible external application on the user's computer. The argument went that by embedding the player into the PDF, and bundling the Flash runtime with Acrobat/Reader, every PDF would work every time. Of course that argument fell apart when mobile entered the game.
The caveats for a non-Flash-Player future are:
As per the ISO standard, right now the configuration you choose in InDesign for how the video/audio player behaves (such as which buttons are on the toolbar skin, whether it loops, etc.) are stored in the PDF in a format designed specifically designed to be understood by the SWF player widget, and anything that replaces it needs to unpick that information. The loop stuff is easy as it's just a text variable, the toolbar "skin" is not as it's yet another SWF file.
As well as embedded files, Rich Media annotations can stream online content from Adobe Media Server using the RTMP protocol - and to decrypt those streams you (currently) need the Flash runtime.
Of course any annotations that display SWF content itself (e.g. animated graphics or games) will be dead on arrival, but those are vanishingly rare given the hassle of making them.
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