To do this we need to follow the below

Get-CASMailboxPlan | fl Name

Name : ExchangeOnline-449cbb2645664646

Name : ExchangeOnlineDeskless-3a08d145664564

Name : ExchangeOnlineEnterprise-a0ce8d44545

Name : ExchangeOnlineEssentials-912457c782-7

Now we need to change the mailbox Plan so that IMAP and POP protocol is disabled by default. I am doing this for Enterprise plan.

Set-CASMailboxPlan ExchangeOnlineEnterprise-a0ce8d44545 -ImapEnabled $false -PopEnabled $false

Now when we create a new mailbox, by default the POP and IMAP protocol for the user will be disabled.