LaTeX Document - would I make every instance of a term internally hyperlinked?
Yes you should. But hide all the links: \usepackage[hidelinks]{hyperref}.
You cannot expect the reader to start on the first page and finish at the last, someone interested in a particular topic jumps to a subsection and will be happy to find a linked glossary term.
Manually linking the terms at the beginning of each chapter contradicts a main advantage of Latex.