So you get less dependant on the grappling hook later? As I said I have not gotten too far, but the grappling mechanic being introduced as a swinging tool then upgraded to an Arkham-like "drag me to this rooftop" (although at specific points so not as free as in Arkham) just killed the game for me. I tried for an hour to get three stars at one of the early time trials, you had to get up to a rooftop and I always came up a few seconds short. Then I looked it up on YouTube to see if there was a route I was missing and saw the guy hookshot to the roof....
Allow me to preface this by saying something: Obviously the grappling hook can only be used in very specific, ordained situations. As such, it's inherently more limited than your other navigational options. However, in the situations where it's more expedient to cross a gap by swinging across it rather than running to the far end of a building to cross a bridge, or zip up a few stories rather than climbing them, it's going to be a smart idea to use it. And the developers want you to use it to attain the fastest speed possible in some dashes. The hook is part of your arsenal as much as the wall run or 180 wall jump is. I don't know why it would bother you to see a grappling spot that you didn't see, while you're assumingly not going to be bothered by missing a panel that could be vaulted off of.
But as far as your question goes, I do not recall a time where I thought there was an obscure hook point to win a trial except in one specific dash. And in that dash, going the manual way was
very obviously not going to result in 3 stars, so it sent me exploring for alternatives. But it should be noted everyone's experience on what's obscure and what's not is relatively subjective. What I might have found to be clear could be the opposite to someone else. That's how these games work.
Regardless, the vast majority of the dashes required me to execute and be precise with other moves and didn't require me finding a cheap shortcut with the hook. I found them to be immensely rewarding and they added to my appreciation of the game.