Organizations with "no org chart" and virtual teams often drop the ball if the managers and supervisors are not well trained in how to manage virtually. I would almost wager that your boss was never really fully trained on managing a virtual team or she never would have gone so long without a team conference call-- that is a huge, huge red flag. While virtual teams and flatter organizations are excellent in theory, they work in reality ONLY if the parties involved stay on top of how to do this form of management. If possible, do some checking - don't be obvious -- into whether the company plans further or regular training for its managers and supervisors; whether your boss's OWN managers check in on how HER performance is doing when running virtual teams; whether everyone is fully accountable in a performance management system that holds managers accountable for failing to communicate issues to employees in a timely manner, etc. Does your boss have a 360 degree review done on her own performance? If you don't know what I mean by 360 degree review, then that's a red flag too; it means that her employees and peers, not just her own boss, get input into her performance review.
I would check into how seriously the organization is really taking its virtual and "no org chart" structure.
And yes, I would do as you plan to -- rock that performance (by checking in with the boss a LOT and getting specific, written goals etc. -- writing is vital, it's your paper trail later!!) and at the same time, seek another job and check any potential employers' structures, use of virtual teams, how they do accountability for running teams, etc. And don't be afraid to leave your current job if you find a better one!