As you've figured out, the apparent duplicate emails are actually your Common Thank-you Email (sent for every order) and a product-based thank-you email (sent only for purchases of that product).
The default [%download_link%] included in the product-based email would lead to the E-junkie-generated thank-you/download page for just that one, particular item. The [%thankyou_link%] included in the default Common Thank-you Email leads to the same thank-you page URL that buyers can reach after completing checkout; normally, this would be a consolidated thx/download page for every item in the order, but if you're redirecting to a Common Thank-you Page URL, then the [%thankyou_link%] would activate that redirection.
You can customize what appears in the IFRAME on your site's thank-you page by customizing your E-junkie Thank-you pages, as the IFRAME method simply displays the consolidated thank-you page content (sans header and footer) that we would normally generate for the full order. This help page explains how to customize your E-junkie-generated thank-you pages and documents what template variables you can use:
Since E-junkie is not a payment processor and does not handle any actual payment funds, we cannot generate or issue a true payment invoice or receipt; typically the actual payment processor (e.g. PayPal, Google Checkout, etc.) would email a receipt email to the buyer separately. The Invoice ID included in our default Common Thank-you Email just identifies the buyer's cart instance as reference for their particular order without disclosing their Transaction ID, so they have a reference in case they need to contact you about their order.