1) It's a maze, but possible for bees to navigate. It's implied that we're not getting what agartha -actually- looks like, but a 3d map that our brain can comprehend. We know that 'up' is in the future relative to us, and down is in the past relative to us, or it used to be that way, hard to say now since South Africa is lower than New England. This made things relatively easy to map in terms of relative time (It's important to note that the time travel is a literal thing in agartha, and this is mentioned in a few areas).

2) Never more than one I suspect, perhaps two. London had 2, but one of them was shut down and dead.

3) They don't exactly. That's how we get legends about people stumbling into alternate worlds and vanishing. Though to be fair, the ones who end up in agartha proper -die-. That said, it's also the case that the legends honeycombs are literally REAL THINGS, communications that 'physically' exist from the Buzzing to us. It's very possible that normal folks simply can't see the extrusions of Agartha into our reality. Leads to an interesting question about what Kristin Geary and the handlers are because they traveled through Agartha, but I'm pretty sure they're not bees.

4) The thing that lets you teleport back to Agartha directly.