Why not gate shard farming?
Gatherers can get a new tool and head to increase their stats high enough to farm the new nodes.
A bot won't be able to do that so easy.
Why not put rare "shard/crystal boxes" in these nodes which, once you open them, give you a number of random shards or crystals.
200 water shards and 50 earth crystals for example.

I think high level gatherers should get a bonus for farming shards and maybe even crystals.
But giving them a simple bonus would enable bots to use them too.