No, they weren't. They were running on PS4 dev kits composed of the actual PS4 hardware.
Developer of upcoming PS4/PC/iOS title The Witness Jonathan Blow tweeted:
It is not true as the article says that “all E3 demos run on hi-end PCs”. The Witness was running on PS4 dev hardware, and it looked to me like all the other PS4 games were running on dev kits as well.
Dev hardware is the hardware that will be in the final retail box, but in a less consumer-oriented package.
Dev kits almost always have more RAM yeah. Better CPU+GPU, no…
All the indies I know were running on the PS4.
We worked very hard to get our game running on the actual PS4 hardware and operating system in time for the show. As did many other devs.
If you have any other facts that you'd like to pull out of your glorious PC gaming master race ass and post here, please, feel free to do so.