I have this issue with some mail providers and not others as I currently have 6 different mailboxes setup with a variety of different services. 1 outlook, 1 gmail, 3 imap and 1 exchange.
To restore this functionality this is what has worked for me as the option was missing when using my outlook email but not my other mailboxes, however please read through these instructions first before attempting this as you may need to search online the imap and smtp details from your mail provider but these instructions should be enough to guide you through the steps for setting up the email on your iPhone/iPad.
1. Go to settings >> Mail >> Accounts and find the account that doesnt have the "delete all" option
2. Click the account and at the top above account box it should say in small grey text what kind of account it is (e.g exchange, imap,gmail,outlook)
3. If it using outlook (my offending mailbox) press delete at the bottom and remove it
3. Choose add account >> Other >> Add mail account (This is where you may need to find some details)
4. Fill in the New account details with your Name, Email, Password and such.
5. You will see a new screen with a few blank boxes for "Incoming/outgoing Mail Server".
Your username should just be your email but this may differ from your provider.
You will also need to find these details from your mail provider but the outlook ones are below
Incoming mail server: imap-mail.outlook.com
outgoing mail server: smtp-mail.outlook.com
6.Once completed these details press next and then itll ask you to sync mail and notes, tick which you want and press save.
7. Check your mail boxes and you should have the delete all option back.
I can understand why, but when using the automatic setup options for select mailboxes, it stops this option. but ive had 100% sucess rate in switching them to use imap. However I can't say that this will work for everyone but its certainly worked for me and im hoping maybe it'll work for someone else if they are having this same issue, as it seems to be driving alot of people crazy at the moment with iOS 10 removing this function.