Hi,
By "Currently there is an ETA custom field" I suppose that you mean that you have a custom item field that you fill with the ETA for each product in each order in the backend.
A custom item field can be displayed automatically below the product name in the "order status notification" (sent when the status of an order is changed), or the "order notification" (sent when you use the "email" button of an order.
So supposing that the email display settings of the custom field are activated (menu Display>Custom fields), that information can be added to the emails automatically without changing any code or doing any customization. It will actually be displayed by the tag {LINEVAR:PRODUCT_DETAILS} in the HTML version.
Now, you can indeed use the {LINEVAR:item.eta} tag to display it without letting the system display it for you, but it has to be displayed between the <!--{START:PRODUCT_LINE}--> and <!--{END:PRODUCT_LINE}--> tags of the HTML version of the email.