The general pattern is: <number you have in this slot>/<max stack size>(Total:<number of normal quality ones you have across all slots>[/<High Quality symbol><number of high quality ones you have across all slots>])
(The last part of that, with the high quality number, appears only if it's an item that has normal quality and high quality versions. So with crafting shards, since there's no such thing as high quality, there's only one number in the "Total" section.)
But that "number you have in this slot" only makes sense when you're looking at your inventory window and select a stack of items. It seems to always just show a 1 when you don't have a slot selected (such as when looking at an item in one of the gathering windows).
Besides the item tooltip, there's a spot in the upper right of the Logging or Mining window where it shows three numbers. Those are for the selected item: the number of normal quality ones you have / number of high quality ones you have / number of collectible quality ones you have. (While the item tooltip only shows High or Collectible quality numbers under its totals on items that actually have those quality tiers available, the Logging/Mining windows always show all three, even where they don't apply. So a crafting shard, for instance, would always show 0 High Quality and 0 Collectible quality, since shards don't have quality tiers.)
And in the specific case of crafting shards/crystals/clusters, since they have their own special interface in the inventory screen, it's also the maximum number you can hold. (With regular stackable items that use normal inventory slots, you can have 99 in one slot, but your hundredth would simply start another stack in another inventory slot, so the max is 99 times your available slots.) The only way to have more than 9999 of a particular type of shard is to have your retainers hold some of them, since they can each hold up to another 9999.