Not sure. I’m using WP since a while already but just noticed that the indexed article pages URL including /search/ return a 404, but not the others like /tag/ etc…
Okay so if I understand this correctly you want to remove /search/ from the URL when it’s there. That’s simple enough using mod_rewrite.
First though, let’s have a look at your .htaccess
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /blog/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /blog/index.php [L]
</IfModule>
# END WordPress
You should drop the <IfModule mod_rewrite.c> and </IfModule>, you don’t need it; it just slows thing down for nothing.
You can probably drop the RewriteBase as well; just try it and put it back if it doesn’t work.