Shards/Crystals/Clusters (and some other items from nodes) have a blank value for the old "chance at HQ" which is now the "chance for an extra one", thus any skill that effects an item in a node based on this chance will not work on "blanked" items, it just wastes GP.
For Shards/Crystals/Clusters, there are two specific skills for them that last for the duration of the node, The Twelve's Bounty and The Giving Land. The first one increases the items per hit by 1~3 depending on your stats, the other increase the items per hit by X=Random Amount, but has a 3m cool down.
In addition to those two, the Bountiful Yield skills increase items per hit by 1~3 depending on your stats, but you must use it for each hit. The Kings Yield skills increases items per hit and lasts for the duration of the node, but is GP costly.
Generally, however, after using GP for the two specific skills, you may not have enough to also stack the Kings Yield + Bountiful Yield for all the hits you will be making on the node.... I find it faster to just use The Twelve's Bounty and The Giving Land, plus chug cordials.
As for the various "buffs" a node has that effects the amount of items you get per hit or the amount of hits you get on the node, all clusters of nodes will normally have one with an extra hit (as in you can swing 5 times instead of just 4) and one with an extra item per hit (as in for each swing, you get 2 items instead of just one) at minimum. At random, you will get nodes with a larger number of hits buff or a larger amount of items per hit buff (or higher % chance on items with % chance). However, these generally are stat dependent in some way, such as maybe a xxx or higher GP total required, or +xxx Gathering or Perception required. If you do not meet the requirements, which will show on the node window and/or node target, then the effect doesn't apply.
Now, because of the stat requirements, it is actually easier to farm nodes much lower level than your gathering job, as they are scaled to have stat requirement for a gatherer at that node's level.
Crystal farming L90 nodes is less efficient than L60 nodes, as occasionally the L90 node's stat requirements exceed your stats, so you don't get the node's buff effect.
As I said, I generally save The Giving Land skill for a node with either + hits (best use) or + items per hit (second best use), as it has the higher GP cost plus the 3 minute cool down when doing just crystal node farming. Using it on a + node is more efficient use of the GP and the cool down timer.