I tried to clear the cookies, logged out and logged in and still got the problem. If I don't use the search bar, the blacklist works fine and I can see the hidden option, but if I enter something then the blacklist still works but I can't see the hidden option anymore. Can someone help me?

That's due to how the search works.

The main post listing just directly pulls from the database. Since it doesn't actually have to search the database for anything, this is pretty efficient - it just returns posts within that search range. However, this causes a problem for the blacklist: there's no way to filter out blacklisted posts from the database query when we do this. There's two options for how we can make the blacklist still work on the main listing: either we write our PHP code to just not show these options, which is both confusing to users who don't know what's going on when they get fewer posts than they expected if they're downvoted below their post threshold, and creates more overhead on the servers processing the request, or we use JavaScript to hide the thumbnails and leave a placeholder, which makes it obvious why the images aren't showing even if the user doesn't know why they're blacklisted, and doesn't require any additional overhead on the servers as well.

The search, on the other hand, actually searches the database. Since the blacklist is intended to be used to block tags that you don't want to see posts from at all, ever, we include the blacklisted terms in the actual search. Since we use Solr, a text-based indexing software that's very efficient at these types of searches, this doesn't cause much of a performance hit, and it makes the blacklist perform as intended: tags you have blacklisted are completely removed from your Gelbooru experience.

You will not see a "Show hidden" link when you perform a search. The site just doesn't work like that.

The best solution to your problem is to only use the blacklist to block tags you don't want to see at all, period. If this doesn't work for you, there is a workaround: if you directly search for a tag that you have blacklisted, the blacklist will be overridden. For example, if you have the tag "green_eyes" blacklisted and you search for "green_eyes", it'll show you posts tagged "green_eyes" even though they're blacklisted.

Thank you for your quick reply.
Another question: is there a way to save my searches like in danbooru?

You can save them as a favorite in your browser. Otherwise, no.

Thank you very much!
Please help me a bit more: Can I blacklist some specific sizes, for example, I don't want to see any images with height/width below 1000px?

It's in the trac. gelbooru.com/index.php?page=tracker&s=view&id=705

"lowres" is for images below 500px wide and tall.