They're your books; it's not ruining them if you make notes and find value in them.

I don't buy my books as an investment. I buy them to read them. Sometimes I underline or make notations about particularly powerful passages/lines, or I make notes about things I have questions about or to remind myself about something I looked up. Sometimes I make notes about my thoughts about the plot if it's something like a mystery, where I'm trying to keep track of my deductions, etc.

I like seeing my notations later, when I reread the book. Sometimes Past Me gets things SO WRONG that it makes me laugh, but other times, Past Me has interesting insights that Present Me has forgotten about.

I also like it when I buy books and stumble on other people's notations, though; so my opinion about notations is pretty positive.