Hi,
It would not be possible to add the Joomla message system in Javascript because the page is not reloaded.
But, you can access to the javascript code in the hikashop.js file and change the way that the alert is made, with a less intrusive popup system maybe.
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.