Hi,
Custom order fields allow customers to fill them during the checkout. Custom item fields allow customers to fill them on the product page.
There are no custom fields to just display text in the notification emails.
That will require editing the emails via the menu System>Emails and add some custom code to display your text based on the categories of the products in the order. It's not just one or two lines, as you need to go through the products of the order, get their id, load the categories of these products with a MySQL query and then display or not the text based on that.