I got similarly stuck a couple of times revisiting Flashback recently - you encounter locked doors in the game as a matter of course, and they're only ever opened by a switch elsewhere or a key you need to get from an enemy. Except for one door, which looks exactly the same (to my eyes) as every other locked door in the game, but which opens when you shoot it. Didn't think to try that as the game had already taught me it didn't work! Likewise there's another part where you have to shoot a window to get through it, it's a fair chunk into the game, it just looks like background art and no other scenery has been destructible at that point so shooting it never even occurred to me.
That kind of thing, and the Radiator's Metroid example seems really common in old games when you go back to them, I've no idea how we managed to get through some of those games without the internet. I'm pretty sure in most cases I just didn't, and must have been happy to play the first stages of things over and over again.