While an opposable thumb is very useful, I don't think it's necessary for "practicing" intelligence. Cut a man's thumbs off and he'll be seriously impaired, but hardly so much that society couldn't develop tool use, agriculture and technology.
I feel opposable thumbs tend to be brought up on the logic of "this is one of many features unique to humans, therefore it must be related to the important feature unique to humans, which is intelligence". In this case it's not even unique to humans: all Old World monkeys and apes have opposable thumbs to one degree or another.
>I wonder how much the negatives of being short are caused by lower self esteem due to simply what people say and think about heights.
There are statistically proven negative points in being not very attractive in general. Beautiful people have (significantly) higher chance to become successful in their job and/or businesses.