I mean, technically you can destroy a Heartless with other means, even bare handed, it's just not permanent and the Heartless reforms elsewhere.
And given the average strenght and speed of many Heartless types, I don't think it'd be THAT one-sided. Even IF they can't end them for good, for people of the Marvel/DC universes or even the upper power chart of Naruto, they'd be slightly more annoying than a rat infestation.
I don't think even Invisibles would be a concern when you can make a flaming giant that can cleave mountains.
And this is if we assume no other fictional power can act as some sort of Keyblade substitute (which I doubt: even in Kingdom Hearts Jafar was able to block the Keyhole with a barrier). But I don't think there's a definitive answer to that, it's like trying to decide whether or not a Jedi can Force hold -> decapitate every fictional being or not.
Matgsy also has a point: it has indeed been stated in the Reports that the Heartless only react to organic matter, so inorganic warriors might be downright immune.