Technically yes, abbreviation, acronym, and glossary are different things (though a glossary can include acronyms and abbreviations, and in fact, an acronym is an abbreviation). A glossary is just of list of explanations for terms which can include acronyms and abbreviations.
In DokuWiki anything entered (in the correct format and order) into
/conf/acronyms.conf or (more properly)
acronyms.conf.local will display in the way you describe - with a faint line underneath and a mouse-over text showing the full term/meaning. To do so it uses the HTML
abbr (abbreviation) tag.
You may find this plugin useful
acronym4glossary (old, and I haven't tried it),