Arkham City:
Two-FaceKilling School Semester:
Korekiyo and TokoEquestria:
Flim and FlamBarely Survivor:
Tortoise/Hare, Droids, Lindsay LohanAll four games handled this in very different ways.
Arkham City had it as a surprise hydra; the players were unaware that hydras were a possibility. It was done almost 100% for flavor reasons (mods can correct me if I'm wrong here. Killing School Semester still had them as surprise hydra but treated them like different players; the hydrae were introduced after the game had already started and entered the game late as "transfer students". This gave players an indication that *something* was potentially up with them, and the character choices were hints that more than one player might be behind the wheel. This was always an intended mechanic; it was planned that there would be hydras in the game before KSS went into signups.
Equestria was different; there was no mechanical reason for Flim and Flam to be a hydra. What happened was Malkon and Flum both came to me and said that neither one really wanted to play a full game by themselves but asked if they would be able to hydra. The idea amused me so I agreed on the condition that I got to pick their character, and I gave them Flim and Flam as a clue to the players.
Finally, Barely Survivor allowed hydrae as an afterthought but before signups completed. It was publicly known that hydrae would be in the game and furthermore they were intentionally flagged as such by virtue of having "X and Y" names. This allowed players to know exactly what they were dealing with.
All of these games were either Advanced or Complex on the rating scale. In terms of which games should have them I would say that they should probably never be in a Vanilla game and used extremely sparingly in a Standard. If it IS a standard game then they should be limited in number and also expressly flagged out as such to the players.