Hi,
Not sure how well your existing custom upload component handling finding and replacing image files is integrated with HikaShop - if at all - but since you have it, it'd sure be just a minor code amendment in this component for it to find and delete the respective thumbnails as well. Much less effort than developing yet another plugin just for this action. After all, your custom plugin already "knows" the file names, and it's merely about deleting them in a few specific other folders, meaning adding just a tiny snippet of code. No need to "let HikaShop know"... again, it'll know once a thumbnail is missing and will create it then... and only then, anyway.