Hi,
Renaming the hikashop tables is a hard change, and will require you to do a lot of modifications in the HikaShop core files, for all the requests, etc. It's a lot of work. And doing that will cause another problem, the problem of the updates, indeed you will no more be able to update your HikaShop version, because it will erase all your modifications at each update.
Using the custom fields was an easiest solution. It require some changes in the views, but thanks to our override system, you will not lose changes when updating.
When the custom field is created, in the view just hide the input field with some css properties, and add a value in depending on the part it is (shipping or billing), by this way when saving the information will be saved in the database, and when listing the addresses, you will be able to filter on that custom field value.