Risks of developping your own theme from scratch?
if, in a theme developed from scratch, you forgot to provide the code for render some elements, are they going to stay hidden?


Yes, of course - if you develop a theme and override core templates, anything that's left out will remain left out. There's no magic in Drupal, it's just PHP at  the end of the day. Think of it from the other side of the equation - if you were building a theme from scratch, and Drupal kept injecting markup into your templates without your say-so, wouldn't that be a crazy state of affairs?


  Is that because developers forgot to render them manually somewhere?


That's impossible to say from here. Could be that, could be some rogue CSS hiding them, could be a theme override of status messages nulling the output, and a bunch of others besides. The only way to know is to have a look and see what's there.

If the theme follows any sort of convention at all you should be able to look for a variable called $messages for the status messages. Usually it's located in page.tpl.php. 

What you're essentially asking is akin to "I've built a car from scratch, if I leave out the brakes with someone else put them in for me?". The answer is "Only if someone intervenes manually; the assembly line won't do it automatically".