Hi,
To import all the HikaShop data, user and addresses, you can do it via phpMyAdmin.
Import all the HikaShop tables and the Joomla users ones (users, usergroup ...).
This way you will have all you data.
When updating, as you said the customized parts are keeped. But you can backup them and in the views listing just click on the dustbin in order to get the latest version and then apply again you customizations to the views thanks to you backup. Don't copy the content, but see lines by lines what need to be changed.