Hello,
The "why" is simple ; HikaShop 3 was a major release with major modifications and we needed to perform these kind of big modifications in the cart system to make it better in several ways.
The old popup was not flexible, not dynamic, not friendly, not customizable and not extensible.
The new system is using a plugin which allow you and anybody to create a new plugin for its own specifications.
Yes, the new plugin use "vex" popup system (which is now used in HikaShop for a long time) while the old system were using mootools popup (which is deprecated in Joomla for some time).
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.