No, you didn't miss anything at all.
The "Delete All" function is, indeed, gone on iOS 10.
I didn't really use that feature that often while my phone is on iOS 9, so it's a minor impact on my part but sure look likes it's a major one for you.
Hopefully, the function will be back in the next update or so.

Indeed, that's a good question; one which I believe will be part of their "Show-Off-Feature" in the next WWDC kot!
"Hey, look, guys, now you can delete all of your mails ... again!"

This post has been edited by domcobb: Oct 16 2016, 10:48 AM

That's bad!
Which network operator are you with, if you don't mind me asking.