I'll need to find a way to make it easier than it is now, but not so easy so that everyone will discover clues without even thinking about it.
The real problem is that the obsessives are going to find every clue regardless. Whether that means clicking every line of text (and making liberal use of Ren'Py's page back feature), someone making a walkthrough and people just following it, someone hacking directly into the code to see where the links are... people who
want to find every clue are going to find every clue, one way or another.
So what you're basically doing is hiding clues for the people who are mildly interested but not interested enough to care all that much if they miss something (the intersection between the apathetics who don't really care about the clues at all and the obsessives who are going to hunt them all). So what you probably want is something that is helpful for
those people, without worrying about what the obsessives are going to do (like, say, mouse over everything looking for magnifying glasses or whatever).
Other games with "hidden" content do it in different ways. Some have a little indicator pop up on a screen/in a conversation when a hidden clue is present, without explicitly showing what that clue
is. Some have a submenu you can go in to show you which clues you've found, and offer hints for the ones you haven't. But the obsessives are going to game the system no matter how you choose to do it.
You could potentially leave it up to the player to decide for themselves if they want the challenge of finding or just the lazy reward of getting the clues - have a toggle in the menu that either highlights or hints at clues, or doesn't. So people who want the easy way can opt out of the challenge, while people who want to look can just do it the hard way. But then the problem is that most people might just be inclined to toggle easy mode, thus kind of defeating what you're trying to do.
I got the idea from Danganronpa - in that game, sometimes text will appear purple if you want to learn more, but there's absolutely nothing stopping you from clicking on every purple thing to see all the extra info, so why have purple text at all? Just make that part of the normal dialogue.
Reminds me of how Final Fantasy II used dialogue (and how multiple later point-and-click adventures handled parsing). You'd talk to someone, and there would be highlighted words in what they say. Which then unlock those terms for them (and other people), so you can ask questions about those topics. But only if you discover those topics in the first place (for a Mythos-flavored example, you can't really ask anyone about what a Beacon is if you've never heard the term Beacon used before or have any knowledge of its context, but if you talk to someone who mentions it, then you'd be able to bring it up to other people in the future).
But in that case it was intended to encourage exploration of dialogue trees, whereas you're trying to use it for a different purpose. So it's not entirely analogous.