Exclude js file from the bundle by adding the js file in Theme_Directory/etc/view.xml
<exclude>
<item type="file">Mage_Storelocator::js/googlemap.min.js</item>
</exclude>
Exclude js file from minification in config.xml
<config xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="urn:magento:module:Magento_Store:etc/config.xsd">
<default>
<dev>
<js>
<minify_exclude>
<tiny_mce>
/tiny_mce/
</tiny_mce>
</minify_exclude>
</js>
</dev>
</default>
</config>
You have not excluded the files but you have removed them.
So to exclude the files specified by you from merging/bundling you can add those files to exclude list in your Theme_Directory/etc/view.xml so that they can be loaded individually
<exclude>
<item type="file">Module_Name::css/name.css</item>
<item type="file">Module_Name::js/name.js</item>
<item type="file">Vendor_Module::js/name.js</item>
</exclude>
So if you have minified your files please specify the file name as css/name.min.css
or js/name.min.js

I have enabled minification and merge in Magento 2.3.1 and I have excluded this file which is loading separately rather than merge file
<item type="file">Magento_Catalog::js/product/list/toolbar.min.js</item>