Hide Mail from showing in Spotlight but keep Messages
Using the "Privacy" tab in the Spotlight item of "System Preferences" may allow you to add the folder ~/Library/Mail which should remove all email messages from the Spotlight index, at least for email from the Mail.app program. Other email programs like Thunderbird store their data elsewhere and would likely still be indexed by Spotlight.

Generally however the folder ~/Library is not visible, so cannot be navigated through to select ~/Library/Mail unless you something to make it visible as detailed in various places, including http://www.macworld.com/article/2057221/how-to-view-the-library-folder-in-mavericks.html and How do I tell Finder to always show my Library folder on Mavericks?