[TheLastSuperman]

Edit: IF you have already visited:
> AdminCP > Settings > Options > Plugin/Hook System

*And it is set to "Yes" i.e. active then you can try this query in phpmyadmin:

PHP Code:

UPDATE plugin SET active=1 


*This will enable ALL plugins (but before warned it will also enable ones you previously disabled/de-activated) using =0 instead of =1 disables them globally. (Reference Only).
**Not sure what a query is or how running certain SQL can harm your site or make unwanted changes? ALWAYS make a database backup then and you can't go too horribly wrong!

Now check... if it still shows the message (and your not on a cached page like Kevin mentioned) then Kevin is right, there is still disable_hooks code somewhere in a file, check config.php thoroughly.