hooks.php is not a file that belongs to any native WordPress convention. While copying files from parent theme is often mentioned as a technique it only applies to template files, which are part of template hierarchy (native or properly customized one).
Your guess that this is issue of timing is probably accurate. It’s a little counter-intuitive but child theme is loaded before parent theme. So running code on child theme load is too early to affect anything that hadn’t yet happened.
You need to create a function that will run that code and find a good timing for it to be hooked to. after_setup_theme hook might fit, but really specifics completely depend on timing of what parent theme is doing.
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