What a fascinating question.
I've working in various corners of aviation research for a quarter century, and studied hypersonic aircraft design as one of the minor topics when I was an undergraduate. Yet, I can't honest recall ever seeing anything on this topic. Quite a lot on internal interference where an aircraft is affected by its own shockwave, but not on external shock sources.
Now, having said that I've just done a search of a couple of databases not readily accessible from outside aeronautics. I've found one quite informative paper from 1961 which looks into the impact on other aircraft of supersonic shockwaves. If you want to PM or email me an email address, I'd be glad to send it to you - it's from a restricted database, but not actually classified (nor interesting seems to have been even in 1961). It has a grand total of five references, but all of them seem relevant and that might get you down the right rabbit hole.
Have a look on here also - this is a database generally extremely good for pre 1960 aeronautics research.
MAGiC NACA Archive
Now a few other thoughts. I recall Bill Sherlock, who was one of the microlight pilots flying overhead photo-chase on the Thrust SSC talking about the impact on his aircraft (from memory "I thought that something had failed in the wing" were his words). He wrote about that in a few places - possibly "Microlight Flying" magazine?
I'd also have a look at the accounts by pilots who flew nuclear bombers. One man written about quite a lot is Leonard Cheshire (yes, the man who developed charity homes) - he was in the chase aircraft at Nagasaki and there may be things he or other people have written about what they observed and experienced. Aviation historians tend to be prolific, and wading through some appropriate biographies and autobiographies could yield some direct observations from the American, British and French nuclear tests. It won't be hard scientific data, but is likely to be informative and citable nonetheless.
I'd love to see how your research develops - this is a really fascinating research question.
G