In the photos below, the propellers on the B-29 props all stop in the same position. Is this done by hand, it is this automatic?
With the 18 cylinder radial engines in the B-29, a random shutdown would give possible propeller positions ever twenty degrees. They do not automatically stop this way.
However, for staged photos like these, where the appearance of the aircraft is important to those commissioning the image, ground crews would hand rotate the propellers into alignment -- and this was just as much the case in 1944 as it is today.
Notice that the photo of Enola Gay, despite being on a remote airfield, is staged enough that the photographer used a red filter to darken the sky and show the clouds dramatically. This isn't something that was done for just any photograph, because it required several times as much exposure (meaning the camera was most likely placed on a tripod, unlike a common press photo shot hand held).
Per comments, it was also considered a matter of pride, back in the day, to always rotate the propellers to matching positions whenever the airplane wasn't being turned around immediately for another mission. This is in the same category as always having boots polished so the sergeant can see himself, or a bunk made up so tightly a quarter would bounce on the blanket -- operationally unnecessary, but still required.
The props are rotated by hand and are all positioned the same way as follows.
For 4-bladed props: when they are pointing "square" (straight up and down and horizontal) it means the engines have been turned over by hand to work the oil out of the bottom cylinders (i.e., ready to crank for startup). For 3-bladed props they leave the bottom-most blade pointing straight downwards to indicate ready to crank.
If the blades on all the engines are randomly askew it means they have not been turned over by hand and must be thus exercised before cranking to work the pooled oil out, and prevent blowing a head gasket via a hydraulic lock.
One of the pilots of “Doc”, the CAF B29 in the picture, sometimes talks about “indexing” the propellers from the cockpit when ground clearance is needed. For instance, when they taxi at a smaller general aviation airport, they have to shutdown the outboard engines before they can leave the runway. There isn’t enough ground clearance under the B29 props (18”) to not hit the taxiway lights. Before leaving the runway he shuts down the outboard engines and manually “indexes” the propellers using the starter to put them in the X orientation.
This is a consequence of tricycle gear. The B17, for instance, is a tail dragger and thus the props are higher off the ground during taxi.
It's definitely done by hand afterwards. The ultimate proof I guess would be a video of the props stopping, out of alignment, and then a video of folks aligning them later, or just a photo taken afterwards with the props all aligned. I don't have that. But I know there was no mechanism in the B-29 for keeping the props all exactly aligned in flight, so it wouldn't make sense that they would ever stop all in alignment.
Plus, even if hypothetically there was some mechanism to keep the props exactly aligned in flight, it would make no sense that they would always happen to stop in the most aesthetically pleasing orientations ("+" or "x").