As Stan once said when asked the question of the Thing's member "it's a superhero secret".
Best left that way.
On some of the questions asked about the matter...
Does comic Ben use the toilet? Yes. He eats and drinks and has to goes through all that comes with that too, be it standing up or sitting down.
Does he have a visible 'bulge'? No more than any other male heroes in tight costumes manage to avoid having their junk showing through their respective budgie smugglers.
Comparisons to naked Apes? Please....Like werewolves they are covered in hair. Caesar and his other males are
not emasculated
Comparisons to Abomination? Well Abomination was in that film for the end only, and Blonsky was bonkers enough by then to
want the power that came from being mutated, and didn't care about anything else.
Ben however is an unwilling victim of the mutation. Being turned a physical rock monster is enough tragedy. Deliberately drawing attention to his evident castration too is just
utterly stupid (imo).