The easy solution here is to get the link to the file attachment by logging into uStore admin, and click on the product in the orders list. The link will be on the order product details page.
That said, yes, you can edit the email xsl template and add a hyperlink but the uploaded files are by default not accessible to the internet. You will first need to expose the uploaded files to the internet by creating a virtual directory in IIS that points to <installdrive>:\XMPie\uStore\App\uStoreShared\FileAttachments
You will also need to add an message template SQL query to get the name of the uploaded file from the uStore database like this:
SELECT FriendlyValue
FROM OrderProductDialValue
WHERE (OrderProductID = @OrderProductId) AND (DialID = 111111)
(substitute 11111 with the id # of your file attachment dial.)
You can then add XSL to your message template to build the path to your virtual folder, and add the order product id and "/" and the filename from your qurey.
<xsl:if test="normalize-space(//Sqls/FileUpload/Row/FriendlyName)!=''">
<xsl:element name="a"><xsl:attribute name="href">http://<xsl:value-of select="//Sqls/StoreName/Row/LandingDomain" />/YourVirtualDirectoryName/<xsl:value-of select="//Sqls/OrderProductList/Row/OrderProductID" /></xsl:attribute>Download file attachment</xsl:element>
</xsl:if>
Of course you will have to set the name of the virtual directory you created, and to cater for orders with multiple products, you will probably have to adjust the above code somewhat so that the link is evaluated for each order product.
Don't try this at home unless you have the necessary skills with IIS, SQL and XSL or can get help from someone who does...