Are the numbers/amount of gems irrelevant for their stats? It seems to only affect the amount of shards you get?!
Some gems provide the same stat at every level, such as the green gem (20% crit chance). Others scale based on their level, like the blue gem (X health points). If you already have four gems with crit chance, you can shatter the highest-level one for more shards. When you have an excess of blue gems, you should sell the lower-level ones so you can keep the highest-value gem for the blue socketed weapons.
Later on, I will refactor this system, and all gems will scale based on their level. It seems to be a better approach.