Can you not switch off the 404 response just because you have an empty category? Do you expect the category to be populated very shortly? Then you can just have your category text and a little "sorry we currently are out of stock signup".
If the products are gone for good then I would expire it or redirect it to avoid disappointing too many people.

Sounds like long term you should start removing or merging categories anyway because having 1'000's of empty categories is an inefficient use of resources for you (and for Google).

Ignore the 404 errors as they won't impact the rankings of your site. Here's a link to an article that explains more: https://support.google.com/webmaster.../2409439?hl=en

the best and the final solution ever for 404 error
is redirect all 404 errors to main page
if you use wordpress, there is a plugin for that
Plugin Support : 404 to 301 | Joel Says

Don't be panic, if your website has 404 error. It is because 404 error never impact on SEO.
But, for the user point of view you need to redirect all the 404 error page on the home page.