I noticed this same problem immediately after updating. It seems to be a gltich, after one run with no shotgun Barry has been shooting scientists every time with the hog. Not sure what makes him not shoot, however.
Confirmed just now, version 1.31(1)*. I wore the Barry's Head/Suit and Machinegun Jetpack items if it made a difference, and used the Free Ride gadget to ensure I'd get a vehicle. In the 2 runs I got a Hog, both times Barry used his Shotgun like he used to.
A totally scientific sample of 5 tests seems to indicate that this is caused by your jetpack. With the Golden Piggy Pack Barry doesn't shoot scientists on the Hog, with the Machine Gun Jetpack, Laser Jetpack and Rainbow Jetpack he DOES shoot scientists. He did this twice on each jetpack, so I'm pretty sure this is the cause. As to why, I have no idea. The Golden Piggy Pack is the only jetpack I saw that makes Barry not shoot.