It’s been an up-and-down year for New York’s Roundabout Theater Company. Tonys were won and critics heaped praise on nearly everything Roundabout put on a stage this season, but the company ran a $2 million deficit that is likely to result in layoffs and wage freezes. Performances were packed for the revival of Nine currently running on Broadway, but such things seemed unimportant after artistic director Todd Haimes, who has been at the helm of the company for two decades, learned he had a rare form of cancer midway through the year.