1- Design & pedagogy
The use / non-use of glossary links by students can be the subject of interesting research in the field of education. Especially the influence of the design of such links (more or less visible, even not visible at all) upon their actual use by the students. I feel that a kind of ideal compromise should be reached, whereby those links are visible enough to "tempt" the students to make use of them but not so obstrusive as to "jump" into their eyes.
2.- If you would tell me which theme you are actually using and what kind of formatting you would like for your autolinks, I can provide the necessary information.