I have to do massive categories recreation and deletion on a site. I want to know if modifying categories has any effect on Google indexing? Also, will it generate 404 pages that I should care about?
Also, will it generate 404 pages that I should care about?
The 404 pages that you need to care about are the ones your active websites link to. An easy fix to this in your situation is to modify your HTML (webpage code) so that there are no links that point to the 404's. I'd recommend using a link checker. I use Xenu link sleuth, a free download at http://home.snafu.de/tilman/xenulink.html. It will check every single link found on your site for broken links and will indicate them in red amongst the list of other links it has found.
I have to do massive categories recreation and deletion on a site. I want to know if modifying categories has any effect on Google indexing?
Very likely, because then you're asking to index for different keywords.
For example: if your website was all about cars, and now you decide to change it to a website about dogs, then google will likely give your page no ranking for cars, but a decent ranking for dogs since dogs was what you were aiming for.
It may also affect indexing temporarily because you're making changes to the HTML which increases the time TTFB (time to first byte a.k.a. loading time) which google does not like.
I would also update your sitemaps to your site to point to the new valid URLs, and make sure you update your title and meta description tags on the appropiate pages to include the new category to rank for that category well.
Assuming your WordPress site maintains an automatically-generating/updating XML sitemap and that sitemap is configured in the Google Search Console, you should be fine. Consolidating categories will simply remove them from the sitemap as you work and the indexer will drop them out over time.
You should probably generate a custom 404 page for your site that either displays the new category listing or allows users to search your content. 404 is not great, but if you convert 404 views into regular users via the 404 page, you'll get rewarded for it.