Hello,
I don't see specific negative side effects.
There are a lot of different ways to achieve what you need and the usage of the canonical URL is a good one. You can also check that you right have the setting to "force" to use the canonical URL while generating the product links. So the Joomla redirect system will be less used because HikaShop will directly use the canonical.
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.