There haven't been any rumors about the Apple Pencil's features and support, beyond what Apple showed at the keynote (pressure sensitivity, tilt detection, 12 hour battery life, etc.). Since "peek and pop" rely on pressure detection, it's technically possible for Apple to implement it on the Pro with the Apple Pencil.
I wouldn't expect it, though, for two reasons. The first is practical: Force Touch on the Apple Watch and 3D Touch on the iPhones rely on haptic feedback in the form of small vibrations, to give you feedback on your pressure and to let you know that the system recognized it. The Apple Pencil doesn't have vibratory motors built-in. (For that matter, neither do the iPads - one potential block toward implementing 3D Touch on them.) The second is philosophical. Until the introduction of the iPhone, touchscreen devices were primarily stylus-driven. Steve Jobs' quotes about casting aside styluses dealt with interacting with a device primarily by touch vs. stylus. If Apple implements 3D Touch with the Apple Pencil, it will encourage people to start using the stylus as their primary means of interacting with the iPad Pro, which goes against the philosophy that Apple has been building.