If I create a Note in a pdf in Devonthink it seems only to be visible when I have selected Note on the Annotations toolbar – is that correct? Is it possible to make the note content visible just when scrolling and reading the pdf but without having selected Note?
No. The Note Annotation is different since Sierra. It also is a bit buggy in Apple’s PDFKit, so double-clicking it with the Select tool is the only way to view the contents at this time.