How do you know when you need ganglion cyst removal?

Pain. Usually pain and discomfort are the major reasons for patients having these removed.
When it bothers you. Wrist ganglions, tendon sheath ganglions(usually at the palmer base of the finger), and ganglions just proximal to the nail(sometimes called a mucus cyst) are usually treated conservatively with observation, occasional splints, and occasional aspiration. If these methods fail and the cyst is interfering with activities of daily living surgical excision usually relieves all symptoms.
Size, Location. Its obvious that you should remove a ganglion cyst that is pressing on a nerve, artery or tendon, causing functional issues. They can also be removed for pain, or other issues like interference with watch wear. Keep in mind that recurrence rate is as high as 15%.