‘Segmentation fault: 11’ almost always means the process ran out of RAM whilst trying to perform some operation/calculation. This would corroborate with your slow Mail due to the size of the database you're trying to process (or it's just corrupted in such a way).

It may also be worth checking your free disk space, since the VACUUM command specifically requires plenty of space:

The VACUUM command works by copying the contents of the database into a temporary database file and then overwriting the original with the contents of the temporary file. […] as much as twice the size of the original database file is required in free disk space.

^{https://sqlite.org/lang_vacuum.html}

How Mojave responds when an application tries to access this sensitive information; will it alert the user, block unsigned apps or what?

When an application attempts to access restricted directory the user will be prompted with a dialog box explaining the following information:

• What Application
• What the application is trying to access
• Option to Allow or to Not Allow access

Many applications will prompt for a folder or file selection. If you attempt to drag a folder from a restricted directory (from a normal finder window) into the choose a file dialog box, the folder will open as a blank folder with the prohibited folder icon. This will not produce a request permission dialog box.

Terminal

The exception to asking for access is Terminal. If certain Terminal commands attempts to access these directories they will be blocked automatically without a dialog box.

$ sudo  cp  -r  ~/Library/Messages/ ~/Desktop/test
cp: /Users/[User]/Library/Messages/: unable to copy extended attributes to /Users/[User]/Desktop/test: Operation not permitted
cp: /Users/[User]/Library/Messages/: Operation not permitted

When attempting to use the zip command the directory is ziped up, recursively, until the blocked directory at which it will appear to be empty.

 $ zip -r  ~/Desktop/imessage.zip ~/Library/Messages/

Screenshot taken of finder after unzipping (~/Desktop/imessage.zip) and opening. As you can see it is empty.

Exceptions

If you would like to add exceptions to give certain apps unrestricted permissions this can be done in System Preferences.

1. System Preferences>Security & Privacy>Privacy
2. Unlock if needed
3. Select type of permission
   • Location Services
   • Contacts
   • Calendars
   • Reminders
   • Photos
   • Camera
   • Microphone
   • Accessibility
   • Application Data (Includes Message data, Mail data, etc.)
   • Automation
   • Analytics
4. Click the + icon
5. Select your app
6. Press Add

Note: The application will have to be restarted for changes to take effect.

Warning: Adding terminal will give all terminal commands access.