I have two email accounts including the default one, in dashboard it shows 3/3, in email accounts settings it shows 2/3. And my account was created only two weeks ago, after cpanel to directadmin migrationYou have two created (one on each of your domains) plus the default one (which technically is the same for both domains) this makes your total amount of email accounts 3. This is therefore correct (we set it to 3 to account for the default one, before we moved away from cPanel you had a limit of 2 on the account, unless perhaps you had a really old account which may have had different limits set).
I get it now, thank you. It's just that extra email account wasn't showing up on dashboardYou have three in total. You have two domains. Both of these have one email created.
Under email management, at the top area you have a drop down where you chose which domain to administer, if you click between the two domains you have on your account, you will see that both list one created and one default (the default is aliases of each other so technically the same email address), used primarily internally to allow the system to send messages to you as account holder.