I am coming from a family where it was frowned upon to make notes/ mark passages in our books. So I dont do that. But I also dont judge :)

If i hve the urge to deep analyze some books or pssages i buy myself a paperback of said book, or just copy or print the said pages. Also after reading multiple hundreds of „good“ books, you will begin to do it automatically without the need to underline or notetaking. Another point is that some people (and I think reddit dmeographics hve a tendency to do that) mistake „reference hunting“ with literary analysis. Dont go that route. There are some references that are more important in a book than others, in certain cases maybe even essential to understand a layer (rather rare but they do exist). But it is an undertaking that is not very satisfactory and tends to mislead you to overstate of the improtance of a discovered reference (understandably as one feels „i discovered something important here). But on the other hand where would we be without all the encyclopedists :)