Hi,
If you do a lot of reading to the database and only a bit of writing, using MyISAM is recommended. And that's normally always the case on Joomla/HikaShop websites.
There is no reason to move the HikaShop tables to InnoDB.
But it should not be a problem to do so. It will just make the processing a bit slower if you have a lot of traffic but it's more a server issue than an application issue.