Neither Yootheme nor Gantry templates are built on Bootstrap. Both are using proprietary grid systems, Yootheme = UIkit, Gantry = rt-grid.
Stiil it's possible to get good results, fully responsive, etc. For a start, turn Bootstrap in HikaShop off - YT or Gantry cannot deal with Bootstrap 2 classes, anyway. For perfect results, a couple of views in HikaShop need to be edited to add those proprietary grid classes. A clear understanding of the grid systems, HTML and a little bit of PHP knowledge are required, or a frontend designer with these skills should be hired for these perfect results, and in case of "do-it-yourself", any detailed questions or trouble you should turn to the template providers and ask them. After all, no developer of extensions can prepare code for all the proprietary templates out there.
So, in any case, HikaShop can't be blamed or held "responsible". Joomla 3.x is built around Bootstrap 2, which HikaShop is compatible with - set it to Bootstrap and switch to the Joomla Protostar template for proof.