Let's think about two contexts.
1. The scientist uses this method on his or her notes
This is mainly because ink lasts longer than a soft medium like graphite, it does not fade because of manipulating the notebook (Imagine that the notes you made in a trip by sea to another part of the world, just smudged away because of the paper was moving). And the way to produce shades is using lines with different separations, "etching".
What you see now in for example DaVinci's work are photos of the original artwork, not from a "reproduction".
2. It is used for reproduction
There were different methods of reproduction. In the first period after the invention of the printing press (and even before that in China) xylography or woodblock printing was the main method of carving an illustration. The same, the easiest way to produce gradients is by using lines.
But the real etching is made on a metal plate, not wood, and it is a newer invention, because of the advances in chemistry, mainly acids and its relation to metal plates. There is a similar method called engraving.
Now, for reproduction, some recognized artists would make the work directly and a lot more would be made by anonymous artists, some even signing as the master. In scientific books, the printing process was made later using the notes from the author and reproduced by staff from the publisher.
In your question, you are mentioning both types. Some scientific notebooks and Dante's inferno, that was a series of plates by Albrecht Dürer, meant to be actual plates and woodcarving for reproduction. https://en.wikipedia.org/wiki/Albrecht_D%C3%BCrer#List_of_works
I must say that etching has a "nice feeling", the drawings are meant to be precise in nature. Painting has a bit of "randomness" in the way it reproduces "reality".
In modern days you would use vector drawings for scientific notes, and not digital paintings, for the same reason. And also for the same reason, some drawings would be re-made by some artists using the sketches by the author, if you want a better-looking book.