Yes, the custom fields in HikaShop are stored in the user table of HikaShop.
That is necessary since you can have a "guest checkout" mode in HikaShop where there is no joomla user account created for the user during the checkout while still asking specific user-centric question to the user.
Also, the fields in joomla are usually used to enter the address of the user. However, the address custom fields of hikashop are stored in another table: the hikashop_address table. That's because one user can have several addresses in HikaShop which is not something possible with the joomla fields.
Finally, all the fields in Joomla and the fields in HikaShop can have different names and different proposes, you can create new ones, some of them are not stored in the same way (for example the country/state which is based on the hikashop_zone table in HikaShop)
Because of all that, it gets quite complex to have a synchronization between both system. It's not impossible, but it takes a lot of time. So it's not a priority for us at the moment actually.
What users usually do instead is that instead of the joomla registration page, the use the hikashop registration page so that the data of the fields goes directly in HikaShop and don't use the user profile plugin.