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Yes because image var is set after that hook is called registered by you so reflection of that in code

 

if (false !== Configuration::get('PS_LOGO_MAIL') &&
                file_exists(_PS_IMG_DIR_ . Configuration::get('PS_LOGO_MAIL', null, null, $idShop))
            ) {
                $logo = _PS_IMG_DIR_ . Configuration::get('PS_LOGO_MAIL', null, null, $idShop);
            } else {
                if (file_exists(_PS_IMG_DIR_ . Configuration::get('PS_LOGO', null, null, $idShop))) {
                    $logo = _PS_IMG_DIR_ . Configuration::get('PS_LOGO', null, null, $idShop);
                } else {
                    $templateVars['{shop_logo}'] = '';
                }
            }
            ShopUrl::cacheMainDomainForShop((int) $idShop);
            /* don't attach the logo as */
            if (isset($logo)) {
                $templateVars['{shop_logo}'] = $message->embed(\Swift_Image::fromPath($logo));
            }

You can try by adding actionGetExtraMailTemplateVars hook and add at same index so while merging it update that var and reflect your new image 
 

// Get extra template_vars
            $extraTemplateVars = [];
            Hook::exec(
                'actionGetExtraMailTemplateVars',
                [
                    'template' => $template,
                    'template_vars' => $templateVars,
                    'extra_template_vars' => &$extraTemplateVars,
                    'id_lang' => (int) $idLang,
                ],
                null,
                true
            );
            $templateVars = array_merge($templateVars, $extraTemplateVars);