The history limit is a pane attribute that is fixed at the time of pane creation and cannot be changed for existing panes. The value is taken from the history-limit session option (the default value is 2000).
To create a pane with a different value you will need to set the appropriate history-limit option before creating the pane.
To establish a different default, you can put a line like the following in your .tmux.conf file:
set-option -g history-limit 3000