I am sorry for the delay in answering your question. Org Chart doesn't support so enormous number of subordinates. As average, the maximum number of ones can achieve approximately 300 and it depends on PC performance and browser you use. There are no plans to implement support of a greater number of subordinates. Though not all ones are displayed, all of them can be found with a search.
I would advise you whether to decrease the limit per node and use different sorting order and filtration to display employees you need or to split them into groups under one manager. The last option means that you need to create "fake" managers that are subordinates of the real one, and all employees should be distributed between those "fake" managers as their subordinates.