All server-side email, i.e., email stored within your email accounts is backed up nightly. Nightly email backups are part of your accounts’ nightly backups. Nightly account backups are retained for up to 90 days in the past and are available for direct access or restoration.
If you connect to your email account using an email client (program) using the IMAP protocol, you essentially leave all email on the server (this is the recommended way to setup your account). This is ideal when you access your email using multiple email clients like your Mac, iPad and iPhone. IMAP keeps your devices in sync and your email is accessible from all devices, always.
Email accessed via an IMAP client can occasionally be archived locally (on your computer) by software like MS Outlook to free up space on your server. This is not recommended if you have a single point-of-failure (your computer) or very few backups of your device.
If you connect to your email using the POP3 protocol, your email is downloaded every time you connect to your mailbox (via your email client). In such a configuration, the only email left on the server are new emails that arrive after you last check your email, or ones that are marked for deletion after a certain amount of days have passed from the day they are first downloaded (this setting is available in most email clients).
If you check your email using Webmail (provided with your email account), you never need to worry. Your email is always stored on the server and is backed up when account backups are run.