You can edit the code in the receipt templates so that the qty is included. Go into WA_Universal_Email > Email_Templates and WA_Universal_Email > Templates and look for these files:
receipt.php
pp_receipt.php
In these files do a search for this line of code, it is around line 36 or 45
<?php echo $WA_Store_Cart->DisplayInfo("Description"); ?></td>
You will want to update this line of code to be like this:
<?php echo $WA_Store_Cart->DisplayInfo("Description"); ?><br />Qty: <?php echo $WA_Store_Cart->DisplayInfo("Quantity"); ?></td>
This will get the quantity to show in the email receipt.