The M1 was only introduced in the mid 60's. Until then it seems sekstants where used, to which this seems to be a direct equivalent. By then electronic transistorized analog computers doing stuff like this was pretty trivial tech.
The Space Shuttle core memory was because it was non violate first and foremost, and then also because it has natural radiation hardening. You'll have to link me to somewhere saying that the Shuttle also used a mechanical flight computer. That wouldn't make any kind of sense. Especially since it is a research vessel and can use radio reliably for the same means.
The bell around the mechanical computer was already plenty shielding for the heights the B52 flew, and could have been made smaller and lighter if electronics where used.
The thing with EMP could be a probable explanation but there are still plenty of electronics in a B52 that would have been affected. Also sheilding could have been employed.
Edit: Minuteman 1962
https://en.m.wikipedia.org/wiki/D-17B#And that was a digital unjamable computer, for a missile.
I still think an
analog electronic computer would be better in a B52 since it is essentially a stream processor and have to react very quickly and reliably for many years.
Analog computery stuff is still used in many many places. It's just not fashionable to talk about. ;-). An example is the tracking in a harddrive. A digital system would be to slow and inaccurate to react there.