Samus previously offed Ridley in situations where despite the odds, Space Pirates could bring him back and raring to go. The appearance of the Robo-Ridley is a proof of concept, and Meta Ridley is a complete testament to it. And after seeing the **** Metroid Prime pulled to revive itself, Samus could reasonably conclude Ridley revived himself in the same way in time for Super Metroid.
But with his death in Super Metroid, all of Planet Zebes and the Space Pirates went down with him. No cybertech to artificially revive him, no Phazon to asspull him back. Ridley was killed in karmic fashion - killed by a girl he made an orphan of, looking for the creature that imprinted on her as its mother - and he should have been done and over.
Except he wasn't.
Despite the rational odds and even the impossible odds Ridley still found a way to come back. That's why Samus freaked the hell out (which even then was just for a split second in real time and was prolonged onscreen for drama reasons). He was known as the Cunning God of Death, and Samus saw firsthand just how far Ridley would go to keep that title.