Hi,
Unfortunately, you'll have to do that change for each view file where the thumbnail is displayed.
So it could lead to a lot of changes: the product listings, the product page, the emails, the cart module, the cart view in the checkout, the cart details page, without even talking about the backend.
And each time the modification will be a bit different as the variable names are not necessarily the same.
To know which view file you want to change, you can activate the "Display view files" setting of the HikaShop configuration. That way, you'll be able to easily see which view file is used where (as it also depends on how your shop is configured I can't say for sure).
Then, you can edit them via the menu Display>Views.
I'll give you an example with the main image on the product details page. It's displayed with the code:
$image_options = array('default' => true,'forcesize'=>$this->config->get('image_force_size',true),'scale'=>$this->config->get('image_scale_mode','inside'));
$img = $this->image->getThumbnail(@$image->file_path, array('width' => $width, 'height' => $height), $image_options);
As Jerome said you need to add the 'background' option there.
So it would look like that:
$image_options = array('background'=> "#000000", 'default' => true,'forcesize'=>$this->config->get('image_force_size',true),'scale'=>$this->config->get('image_scale_mode','inside'));
$img = $this->image->getThumbnail(@$image->file_path, array('width' => $width, 'height' => $height), $image_options);
where #000000 is the color code for black.