“If I set my monitor to 1:1 or aspect, then it displays 720×480 exactly as is in the right ratio.”
Ah, nice for you, many monitors don’t have this option, not to mention TVs. There it’s either 4:3 or 16:9; neither one of those options would be work out like that.
(Addendum: Actually, my monitor behaves like that too – there it’s either 16:9 or “Aspect”; 4:3 isn’t possible. That’s why I just ordered a new monitor xD)
“I find it hard to believe that developers didn’t know about this, I don’t think Nintendo used special weird monitors when testing SNES games.”
Maybe they knew, but they didn’t care. Like with all the PS1 and PS2 games that look slightly squished cause they behave as if they were displayed on a 640×480 4:3 display.