Is it permissible to say to someone: "May God grant you a thousand mercies (or good health)"?

There is no religious impediment to this supplication. It is among the best prayers a Muslim can make for himself or for others, as the Prophet, peace and blessings be upon him, guided his Ummah by saying: "Ask Allah for pardon, well-being, and sustained well-being, for no servant has been given anything better than sustained well-being after certainty." The mention of a number in it is for emphasis and abundance, not for specific limitation.