So I deleted thousands of old articles in my site.. but then I got missing urls 404 on the search console website.
It sounds perfectly normal.
Now I've noticed that seo is a mess, some popular urls rankings have gone down
Are you sure this is related? Eventually, the pages you deleted removed internal links, but I doubt they account a lot for your ranking.
At least, be sure that your sitemap no longer includes the pages you deleted, also verify that your other pages are not linking to these deleted ones.
I don't know if this is a good method, but if want to remove a page from a search engine, I use the "noindex,nofollow" meta tag, and leave it at least for a whole year, then eventually I delete the page (404), or replace it with a message, saying the content is no longer available, and with links to other sections of the site, but keeping the "noindex,nofollow" tag.
If the suppression of a page, is because the content was merged with another one, then I use a 301 redirection.
