The two parts are the index and the glossary. I think this works best when the two are not separated.
We go to an index to find out where in the main document we need to go to learn about a specific term. Hyperlink a term to the index when you want the reader to find a specific concept, principle, or formulation associated with the term by going backwards from the index itself. Otherwise, do not hyperlink.
The first definition of a term within the main document deserves hyperlinking into the index. That may sometimes not be the first use of the term.
Example
In below, terms to index are in [ ], with {this sub-link} as the message. Reappearances of that term not put in the index are in ( ).
An [atom]{smallest unit of matter} is the smallest unique chemical constituent of any matter. The (atom) cannot be divided to smaller components with unique chemical behavior. The [atom]{its fundamental particles} contains protons, neutrons, and electrons as its base fundamental particles. The [atom] does not directly contain muons, or gluons, or bosons as its base fundamental particles. An example of the unique chemical nature of an (atom) is its participation in a chemical reaction. One [mole]{with substances} of a substance contains a defined number of [atoms]{atoms in a mole}.
Now that we have the index, build the glossary. Use one (bi-directional) link between the glossary term and the index term. This can suffice to provide both one place to find the term (the index) as well as one point of reference to find the glossary term from any point where it is indexed.
Example
The glossary might say this:
[atom]{link to index term} - The smallest unique chemical consistent of any matter.
...
[mole]{link to index term} - A unit of substance that contains a defined number of physical or chemical things.
... and the index might say this:
atom
- [definition]{link to glossary}
- [smallest unit of matter]
- [its fundamental particles]
- [atoms in a mole]
mole
- [definition]{link to glossary}
- [with substances]
If you do not build both an index and a glossary, then only reference the glossary term in a bidirectional manner at that point where you define the term or first use it in the main content. Other hyperlinks would be redundant. Why? Presumably, if this is going to ePub or PDF, the final document will have its table of contents sidebar that can be used for navigation at any other point.
References
Follow ups for the mechanics of doing glossaries can be directed to the TeX StackExchange, perhaps especially referencing practices with the glossaries package.