Each type of unspoiled node will pop at a specific time of the game day, then vanish 3 game hours later, or after you've used the node in full. Whichever comes first. But yes, there is a pattern. For example Astral Rock will always spawn at 9pm, Darksteel Ore always at 1am, Gold Sand always at 5am, Gold Ore always at 9am, and so on, and so on.