Can one fully remove certain applications from OS X?
If you use any third party email app, you can configure in settings to open that email whenever you click an email link in any other app. To do so, you need to go to general settings of that very third party app and find the option that is usually listed as "Use (app name) as default mail client". 

For instance, I'm using Nylas N1 and wehen you open the app and go under "preferences">"general">Workspace and check "Use Nylas as my default mail client". 

If you tell me what app you are using as your default email client, I could help you find how to enable it, but it shouldn't be too much difference with any app.

As for removing systems build in apps: On OS X 10.10 Yosemite and earlier, it was possible to open a terminal window and issue commands to delete these system apps, which are located in the 
/Applications folder. For example, running the following command in a terminal window would delete the built-in Chess app. Be very careful when typing the following command:

sudo rm -rf /Applications/Chess.app


As of Mac OS X 10.11 El Capitan, System Integrity Protection protects these applications and other system files from being modified. This prevents you from deleting them, and it also ensures malware can’t modify these applications and infect them. If you actually did want to remove any of these built-in apps from your Mac, you’d have to disable System Integrity Protection first. I don’t recommend that. However, you can re-enable SIP afterwards and your Mac won’t mind that you’ve deleted Chess.app and other built-in system apps.

Really, I recommend you, don’t do this. Mac OS X may automatically reinstall these applications in the future when you update the system, anyway. They don’t take up much space, and Apple provides no way to get them back beyond reinstalling OS X on your Mac.

This doesn’t actually erase an application’s preferences. Erase an application and it will leave preference files left over in your Library folders. Most of the time, these files will use very little space and won’t cause a problem. The preferences will still be available on your Mac, too — this is convenient if you’re uninstalling an app only to replace it with a newer version of the same app.

Hope this helps.