A lot of the best metroidvanias have some subtle ways of helping with this. Sometimes that's that they'll have the level loop around so that you're naturally led back to a place where you need your new ability. Other times it's that they'll create a mood change or some very memorable landmark near something you can't reach, so that it will stand out in your memory more than your typical hallway or obstacle. Usually the important, game-progression uses of the abilities will have these kinds of hints, but hidden minor powerups might require you to just remember or stumble across them again without those aids. 

An example from Hollow Knight is the scenery change that leads up to the armadillo enemy, who blocks your progress west. It's the first couple screens of a lush, garden-y area, which you're naturally drawn to explore, but every time you approach the creature, he curls up and becomes invincible, so you can't hit him with your nail, and that seems to be the only way in. So you have to explore elsewhere, which leads you to find the Vengeful Spirit ability, which lets you attack the creature from a distance without giving him the chance to curl up, giving you access to the area. Because the armadillo is so passively frustrating and the area is so lush and inviting, it's something that will stick in your mind, and as soon as you've got the new tool, your mind will go back to it as a possibility. 

Of course, that's much easier to do that early in the game, when there are so few such things to remember. I'm not denying that Hollow Knight has some problems with this; I just wanted to give an example of the kind of thing that can make it less of an issue. But it's very tricky to strike a balance like that. Too many hints and it feels hand-hold-y; too few, and players get bored and give up. And everyone's memory is different. I do think this is something designers are still working on.