Hi,
Well, if you enter 0.001 for the shipping methods with free shipping, and then change the translation of "free shipping" to "TBD", you'll get TBD for these shipping methods and you'll get 0.00 for your other free shipping methods.
So what I proposed should be ok.
Now if you really want to do what you suggest with code modifications, you can do that in the function getDisplayPrice of the file administrator/components/com_hikashop/helpers/checkout.php
Note however that you'll loose the changes there after each update.