Bee hives are pretty unfriendly to bot. They take a bit of luck/finesse to solo, are pretty easy to duo, and ultimately you still need to find the things. They are certainly difficult to do naked early world, which is effectively where throwaway bots stay forever.
Option 1)
Localized resources spawn small swarm guardians of varied numbers (or maybe none like hives) when the resource is raided. Sometimes it spawns a bigger/tougher guardian that drops loot or guards a bigger cache can appear. This kind of on the fly decision making is significantly harder to bot.
Localized resources are notably more common, but you get smaller fragments to compensate. Instead of getting a whole piece of salt, you'd get 0.1 or some such that needs to be piled together. The "luck" would be in finding a good resource node that spawns a bigger guardian. I think this would lessen the need for scout bots. I'm assuming to control spawn rate, the rare forageable stocking system would be put into place. These would not be permanent spawns in the world.
To further reduce alting issues, they could require a specific stat to either see them and/or harvest them. Only masons of Masonry*Per X would be able to see rock crystals, etc. Could give additional utility to perception. Because they're sort of a group raiding event potentially, maybe it would be the character who loads the map that decides if it's seen, but once it's spawned it's visible to all players in the area? Or it could become visible once someone tries to raid it for the first time.
Option 2)
Localized resources spawn like a meteorite (without the global pop up). When spawned they get a timer before opening to be harvested. This way anyone who passes by would be able to see the timer and decide if they wanted to show up.
Same beehive swarm guard style defense that applies as Option 1 to prevent naked alts grabbing the resources. Same chance to occasionally spawn a miniboss (which would only spawn once on the first raid attempt, with swarmers spawning for anyone else who tried to raid that after).
Resources would be static like dungeons, present until someone completes raiding it.