@Coolnessda your most efficient use of crystals would be to use 150 per day refreshing energy. Either normal or ship energy, or split between them.
As others have said, farming shards from nodes is by far the most crystal efficient way of gaining shards.
If you are not in a hurry to get a particular toon, then farming multiple nodes will get you further in the long run than refreshing nodes. Those 25 crystals to refresh a node is a big chunk of your 170 per day.
You'll build up a small amount of crystals that you can use to get them pesky golden eyeball components.