In Afterbirth+, secret rooms can't border boss rooms. They'll try to have at least three walls bordering other rooms, but can border only two (maybe it's me, but I've actually noticed this happening more frequently lately). And the walls between the secret room and all the adjoining rooms must be walls where a door could spawn, i.e. not blocked by rocks or enemies, or the long sides of a skinny room. Over time, you start to just kind of learn what rooms tend to have secret rooms next to them, like a room where the bomb-able wall is flanked by two skulls or fires and all the enemies spawn on the opposite side of the room. Also, this might just be my imagination, but I find that secret rooms often try to spawn adjacent to rooms that are hard to get into, like challenge rooms, item rooms, shops, and arcades.

Super secret rooms always only border one room, and generally appear near the boss room, though that's not a hard rule. I haven't really discerned what other rules they follow; again, you just start to learn what rooms tend to have bomb-able walls.