Yeah, Dedede beats Shao Kahn. Let's run it down.
Yes, Kahn is intelligent unlike Dedede, but he is arrogant. Sure, Dedede is clumsy, but he uses his clumsiness as an offense and isn't as arrogant. The only benefit from Kahn's arrogance is that it heals a small amount of his health.
As for strength and destructive powers, they're kind of swapped. Kahn's hammer is powerful and can destroy a human in one blow and is very strong himself in a fistfight. Dedede's hammer is not as powerful, but can destroy a building and create shockwaves. Besides, Dedede can inhale objects and projectiles as well, so Kahn's projectiles don't mean much to him. Masked Dedede was also a strong point for our penguin friend. Still, they're both strong and hold capabilities, but one has more than the other (Kahn has more strength / DDD has more destructive powers). Besides that, Kahn usually goes into battle with his fists rather than his hammer as a main tool, where instead he brings it as an attack.
Kahn faced so many Kombatants, but how strong were they? Since he lived for such a long time, probably not strong enough where Kahn can't handle it. But for DDD we have the time he destroyed Dark Meta Knight,a stronger edgier Meta Knight, who unlike the original one, ambushes his opponents and leaves them helpless before slicing them into pieces. Other than that, Dedede fights Kirby on a daily basis, and that ****** can crack planets in half.
Durability is also even between them. DDD may have taken a planet-sized explosion like Kirby as well, but then there's Kahn's stand against and Elder Gods infused Raiden blast which did nothing.
Now speed is where Dedede takes it. He literally dominates the skies flying at lightspeed. Meanwhile, Kahn's only real source of speed are his charging attacks and teleportation. But the Charging Spike doesn't go too far, and the only time he teleports is outside of battle, but when he does, he has to walk out of a portal thing.
Now let's talk about Experience. Of course, Kahn has been absorbing souls for so many millennia, and he has killed so many people along with it. Dedede, although he has been seen mostly helping on adventures, but has been solo adventuring before whether it's a New Game+ mode where he replaces Kirby or it's Dedede Tour. But Dedede does not come close to Kahn's years of ruling.
In the end, Dedede mostly wins because of his major speed advantage and Kahn can't really do much against a flying Dedede, so he'll just taunt him and leave himself wide open before the next thing he knows he about to get clobbered.
DEDEDE - Winner
+Faster
+Not as arrogant as Kahn
+Advantage in the Air
+Can inhale Kahn's projectiles
=Equal in Strength and Durability
-Not too smart
-Clumsy
SHAO KAHN - Loser
+Way more experience
+Advantage in Hand-to-Hand Kombat you see what I did there?
=Equal in Strength and Durability
-Arrogance blinds him
-Underestimates his foes
-Slow