No one’s mentioned ‘We’ll Sing In the Sunshine’ by Gale Garnett? A warm, homey, sunny-honey of a countryish song, conjuring up images of strolling down a lane, hand in hand, alongside a field of sunflowers. And yet, the singer is saying loud and clear ‘I will never love you’ and ‘I will stay with you a year and a day, and then I’ll be on my way’. Rather cold lyrics set to a lovely warm song.
I think it’s a mistake to ever think of “tendency tones” as a separate issue. They are nothing but a piece of the explanation of what “key” means, and an aspect of how harmony operates. Like saying “That’s not chemistry, that’s just a simple ion exchange”. 
My favorite Cheerful Song with Dark Lyrics has to be the Big Daddy remake of Celine Dion’s “My Heart Will Go On”. They recast it as an upbeat, bouncy, Elvis Presley song. It is absolutely hilarious:
https://www.last.fm/music/Big+Daddy/_/My+Heart+Will+Go+On
“Luka” by Suzanne Vega - surprisingly bright & peppy for a song about a physically abused boy.
“Family Snapshot” by Peter Gabriel - while not exactly cheeful, the song’s remarkably upbeat for its subject matter (although I could never determine if it’s about a real political assassination or someone fantasizing about a political assassination.)
I disagree, but we’re going a bit far afield here of the OP, so I’ll leave it at that.
See Wikipedia: Family Snapshot - Wikipedia
“Hungry Heart” by Bruce Springsteen. And written by the Boss: “Out of Work” by Gary U.S. Bonds.
And Petula Clark's "Don't Sleep in the Subway". I once heard a comedienne say, "What kind of guys does she date, anyway?
This somehow only just came to mind, but searching the thread, I see you mentioned it. I think the Smiths have to be up there in terms of writing jangly, upbeat-sounding pop songs that should be about love and rainbows and puppy dogs, but end up being about much more melancholy subjects.
Belle And Sebastian are also good at this (definitely inspired by the Smiths). The most beautiful melodies, but the lyrics might kick you in the face.
And to finally get it out of my system after having followed this thread for some days now: one of the most obvious examples for this trope hasn’t been posted yet, Bad Moon Rising. A bouncy country-pop song about impending doom, maybe apocalypse.
Yes. Good one!
With the added bonus of directions to the restroom.
I would just say because in general music appreciation is very broad but understanding what you just wrote is a niche subject few people even know about. So people who are fans of music but don’t know about writing or making music make assumptions based on feeling.
How many times has “Semi-charmed Life” by Third Eye Blind been mentioned? Always the first one I think of. Not only that but it always seems like one that people don’t really pay attention to the lyrics or only later discover them. A lot of these are cheerful/upbeat but the lyrics hit you over the head with how dark they are.
One could include almost the entire Rage Against the Machine library here. Not sure I’d consider the music “upbeat,” but it’s brighter than the lyrics.
Should be easy to find, I hear Big Old Jed left the light on.
This song is intentionally structured this way and if you see the video it is obvious, I am mostly commenting because it hasn’t been mentioned yet and is an extreme example.
Amanda Palmer - Oasis
Edited to add:
Any song by the Violent Femmes.
How about Another One Bites the Dust?
Also “Peaches and Diesel” — he cheerfully sings “Boy, you’re gonna he dead!”