Hi,
The "bootstrap" popup use Joomla to include the appropriate content.
Afterwards, I don't know if your template will be compatible or not ; bootstrap 3 does not have a very good retro-compatibility with bootstrap 2.
But, with the next HikaShop release (2.6.1), we will propose a new popup system which is based on jQuery (no mootools, no bootstrap).
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.