well, they exist to gate crafting. If SE completely got rid of timed nodes, they'd implement a different sort of timed gate, such as requiring 99 each of 6 different items to craft a piece of gear.
Also timed nodes make it feel as though our GP and DoL skills are actually good for something. Untimed nodes you can just brute force your way into getting all the HQs you need with 1 or 2 skills