Whenever a glossary is hidden, its entries are no longer available for hyperlinking in any of the course's resources. I agree that it should be possible to have hidden glossaries, but...
However there is a workaround. 
In your course's settings, have more Topics than necessary. Place your glossary in one un-used topic, hide that topic but do not hide the Glossary. The entries of that hidden glossary will be available for hyperlinking but the Glossary itself won't be visible.
Unfortunately, because there is a link to glossary in the entries' popup windows, the students will still be able to access the glossary from there.
To remove that link, see my post here.
Joseph