I have a problem with the Android app, in that I can successfully turn off all notifications for all accounts individually (as per eM Clienton Android - Per account notifications?), but not for one account.
It is a Hotmail account, and for that account only, there is no option to turn off notifications.
Have you tried removing and readding that Hotmail account again to see if that fixes it.
So, interestingly, I found a fix for this.
I was going via the previously spoken about route of going to Android notification settings, where I could then not turn off notifications for this one account only.
But going via the built-in notifications setting for that account within eMClient itself (which I think may be a new option?), I could then access that setting screen and turn them off.