I take the point that they do add more gameplay - but Chapter One was the only one I had them in and they don't add that much. It's a risk that it's more of a chore to actually find these things by having to click everywhere and there are other ways to get content in.
If we look at the three chapters out so far, I doubt many people would say that Three suffered by an absence of clickables for example. So for consistency they'll come out,
I liked the clickables, but do think they needed some kind of a "hey, this thingy is clickable!!" indicator. Like, no indication that Annie's mug is clickable when you just have the screen open, but a thin blue border around it when you move your mouse over it.
(Not sure how to do it in Ren'Py, but I've seen other developers manage to do this, it's probably to do with adding an overlay on some event called "Mouse_over" or something similar. It might need removing again on some other event, not sure.
A possibility is also placing an overlay object (like, a button) above the mug with a transparent texture, which could then have that "Mouse_over" event tied to itself, which then (temporarily) changes its own picture. It varies a bit with each programming language how to do tricks like these, and what the exact event would be called and whether it disables itself, or needs some other trick to disable again.
But seriously, if you can keep the eastereggs hidden, but with just a little indicator, that would be perfect!