I have been using Apple Notes as a "digital filing cabinet" for over a year now and it's fantastic. I have tried so many other apps for this purpose (Pocket, Notion, MyMind, KeepIt, Raindrop, etc). Apple Notes blows them all away with its features, flexibility, and search function. I've compared Apple Notes head-to-head with each of these services and its search functionality alone is always superior. In addition, with Apple Notes, I can scan things in, share individual notes, and easily save and annotate PDFs (like you describe). I use Apple Notes not just for personal things, but also to collect information for research projects.