The get_theme_mod() function could return an explicit false. The === operator looks for exact matches, so in the case of hide_logo not being set the function would return false and false is not an exact match to an empty string ''. The == operator is a bit more forgiving in that sense which is why you don’t have an issue there.
You could supply a default value as the second parameter which will be returned if a value is not set or does not exist:
if( '' === get_theme_mod( 'hide_logo', '' ) ) {}