Since you're posting on the icloud forum, I'm assuming you are referring to icloud mail.
iCloud uses an IMAP email service, and this means that icloud keeps all emails on its servers and syncs them to all devices that connect to the service. In other words, it keeps all devices synced the same (which is what most users want). If you delete an email on an ipad, that will result in it being deleted everywhere, including the icloud servers. That's the way IMAP is designed.