Beavis barging into the cockpit screaming "I AM CORNHOLIO!" was funny in 1996, not quite so funny after 9/11.
Bork finds it hard to believe that Beavis and Butthead are terrorists. Fleming then says "you have no idea what kids are capable of!" There have since been numerous cases of teenagers committing school shootings and terrorist acts, like the 2015 Paris attack.
The whole running gag about cavity searches also smacks of this knowing the unfortunate rise in cavity searches since the early 2000's.
Estranged husband-and-wife criminal duo Muddy and Dallas Grimes are voiced by then-Hollywood power couple Bruce Willis and Demi Moore. They split up not long afterwards. Though for them it's probably Harsher in Hindsight.
The demon girl dancing around in Beavis's hallucination looks a lot like Kneesock.
Les Yay: While being interrogated, Dallas was given a cavity search by Agent Hurley, a big-boned woman. When Agent Flemming threatens to give her another, she looks at Agent Hurley, who's staring back, with a smug and said "Ooh, is that a promise?". She apparently enjoyed it and wouldn't mind another.
One-Scene Wonder: Chelsea Clinton. Only on-screen for a few seconds, doesn't say a word, but the fact that she hurled Butthead out the window implies some serious Badassery.
Beavis and Butthead waking up in the desert to find themselves totally alone, on the brink of death. Considering that the two men in the previous scene were strongly implied to be their fathers, it's a rather sad image.