Jelle
Certainly BOAC continued to overfly Vietnam with their VC10 Hong Kong service well into the War, in common with many other intercontinental airlines, and certainly there were many encounters with B52s and other aggressive types in the area during that period, some quite close and unexpected. It was one of those areas where all hands were on the (flight) deck and all eyes were outside during the transit. Claims were made about bombs being seen to be released but it would be necessary to be extremely close to observe that and I neither heard nor saw any really convincing evidence within BOAC. That doesn't mean to say it didn't happen, or that it was a sensible area for any civil aircraft to routinely operate within at the time - a point strongly made to the airline by some of the crews involved.
Edited to remove stray icon.