If we're talking specifically Danmachi, then I'd go with what Flame said since I'm not up to date on the LNs. In general though, I believe it depends on the intention of the dungeon. If the dungeon itself is man-made, then the number of entrances is arbitrary, as it would have simply been determined by the architect(s). Alternatively, there could be a different explanation if it's a natural dungeon, as in created by the natural elements and processes of the world like erosion or whatever. For example, if it was originally a cave created by an underground water source that developed into a rapids or something which was then inhabited by monsters after the fact, then the number of dungeon entrances would have been originally determined by the forces that created the cave in the first place. If we're taking a living or modular dungeon concept however, then it would definitely be determined by the dungeon's host, the being in control of the dungeon itself. Whatever that being decides is best is what's gonna happen, and the reasoning then boils down to why it was considered the best course of action. As far as whether the entrances can be in any way manipulated from the outside... I suppose it depends on the lore and material makeup of the dungeon. If the material is too advanced for outside forces or, like before, has some kind of "plot armor" such as a forcefield or whatever then it makes sense that something outside cannot affect anything inside. Otherwise, they should be able to.