1) For Spanish, should it be replaced with "Spanish", "es" and "BxSpa"?

Yes, certainly.

2) Should I also change the files that are in modules/boonex/spanish/install, in the "langs" and "sql" subfolders?

Only the content within files, the modules/boonex/spanish/install/langs/en.xml can be left under its name.

3) Instead of editing the en.xml file and then installing the module, I could first install the module and then edit with Polyglot?

Yes, you could. But in this case, you will not use the "Restore all" option in the Developer App.

4) Considering that there are many phrases to be translated, is there a way to identify those that users are going to view in order to start working with those phrases first?

Well, there is no reliable way, except that many lang keys with the "_adm_" word within are visible for admins and moderators.