>>2995233OP here. They're actually portrayed together a lot more than you think.
This doesn't count End of the Line, which is a fanmade SFM, but it can be included if you want.
While Scout and Sniper have different personalities, that's actually what makes them right for each other - no one else but Sniper has the patience to deal with Scout's bullshit.
Spy is too snobby to actually like Sniper, and Sniper has zero interest in the pretentious fancypants lifestyle that Spy has. The only reason that SniperSpy is popular is because of hatesex/angst/whatever. It's been shown time and time again that Sniper and Spy legitimately hate each other.
If you want to get into autistic headcanons, some people believe that Sniper is lonely and appreciates Scout's presence, and if you think about it Scout doesn't really have anyone to talk to. Scout's often depicted to be friends with Pyro but there isn't anything even suggesting that in canon. Hell, he calls him a freak in Meet the Pyro.
But for me, yes, it is because they are the "hot ones"