The % character is a special character in the gettext translation functions. To escape the % character to use it in a string, change it to %%.
If you weren’t using the __() translation functions, then a single % character would give you the number of comments. However, when you are using the translation functions, % is a special character with special meaning. If you want to actually include a % character in the string, you need to type it as %%. The __() function will send a single % on to the comments_number function, and you should get the number of comments in its place.
Your comments_number function should be:
comments_number( __('There are no comments so far', 'hbthemes'), __('There is <strong>1 comment</strong> so far', 'hbthemes'), __('There are <strong>%% comments</strong> so far', 'hbthemes') );