Aqua does not use the standard Android Email, or manufacturer specific Email apps in any way.
It also does not use the accounts there.
Removing accounts from the Email app should be safe and have no side effects -- unlike removing the @gmail account, which gives you access to all kinds of synced data (such as Contacts, Play purchase history, etc.). Luckily, it is possible to disable email sync for the @gmail account in system settings.
Other than that, the "stock" Android Email does have a way to disable mail sync per-account. Manufacturer specific Email apps may vary here.