Ordinarily, the iPad acts as a live mirror of your e-mail account. It's a way to "real time" view emails. Whatever you do on the iPad is going to be transmitted to and affect the server where your mail is stored.
So, that means that yes, e-mail you delete via the iPad will be deleted from the server. And, since you are interacting with your e-mail at the server level, when you delete an e-mail on the iPad, it will no longer be on the server (so you won't be able to download it to your Mac).
However, the odds are that the e-mail you deleted is still on the server in the Trash or Recycle Bin. You may be able to access that trash bin via the iPad to retrieve your e-mail(s). Or, maybe you can use a web-interface on your computer to access the trash on the server directly.
Hope this clarifies and helps.
Marilyn