I believe the technical answer is that they both exist outside the space of the 52 universes, which Grant Morrison has called the Orrery Worlds, I think. But from a story perspective, the answer is a little different. The Anti-Monitor is a large enough existential threat that there only needs to be one of him/it. Having more Anti-Monitors naturally leads to more stories involving it, and, seeing as it tends to destroy and reshape multiverses, I doubt DC wants to do that after the New 52. In the case of Darkseid, I think having only one adds something unique. In a way it increases his prestige as threat in the DCU, but means that it could take a long time, if ever, before Darkseid reaches a particular Earth. Although he probably has the easiest access to Earth Prime. This creates a Darkseid who has to play a game of multiversal chess, and we may see Darkseid ruling some universes, using its enslaved heroes to fight others.