I don' know exaclty how bots work, but it seems like you could outsmart them by making farming more interactive and rewarding an intelligent human interaction while making the brainless fail. Disincentivize mindless botting. Incentivize thoughtful strategic farming or gathering.

Make shards show up in different depths? Add debris you have to clear? Allow an intelligent gatherer to gather many shards in the same time it takes a bot to gather far fewer?