Yes! I write on pen and paper a lot. I've been known for my entire professional life to carry a moleskine with me at all times. This year, I switched to a 2018 iPad Pro with an Apple Pencil. I use Good Notes. I still "hand-write" all my notes but do it on the iPad instead. So far so good I'm in love with it.
In terms of the note structures themselves: each page (I use front/back and left/right) has a title and I just use bullet points and arrows and so on to collect thoughts.
I also preserve my notebooks. I still have the original moleskine where I sketched out Vagrant, Packer, Consul, Terraform, and others! This was back in 2009 or so.