1. Hiding the default Glossary search: You could hide the standard search box quite easily, either by using CSS to hide it, or editing the PHP code to remove it.
2. Using Solr to search the Glossary: you could use a Generico filter to configure a glossary-specific search that used Solr to search the glossary in this course only (see this related post: https://moodle.org/mod/forum/discuss.php?d=434583#p1748773).
3. Using Solr to search linked files on NextCloud: this is probably very hard, and would require a lot of custom development. You should first check whether or not Solr actually indexes linked files on Nextcloud or not. Perhaps it all just works already! If not, then as an alternative, you could instead use Nextcloud, which seems to have its own search facilities, see https://apps.nextcloud.com/categories/search. You could probably integrate the Nextcloud search facility into Moodle somehow, and use it to search the glossary in some way. If you host your own Nextcloud instance, then perhaps you could get Solr to index it and use it within Moodle. You would need to get some advice on this from the Nextcloud people.