Good scenario, huh? What you refer to was actually intended by Harlan and is documented in the readme. Here's the whole quote:

"I did something very peculiar with the Eagle, Ents, Hobbits, Nazgul, Dwarves,
Dragon, and Spiders unit types. At least one unit of all these types exist at the
beginning of the game yet no one has (or is likely to get) the technologies to make
any more of them. You may recall from the trilogy that most of the non-human species
were in serious decline as it was the humans' destiny to dominate Middle Earth in
the coming Fourth Age. So once the starting units of that type are gone, that's it-
the species is basically extinct. However I have made certain exceptions to this:
at the start of the game some cities are in the middle of producing some of these
special units. Such a city can keep making that unit forever but if one ever changes
the production in that city to something else it will never be able to make that
advanced unit again. So be careful! These cities are:

Hobbiton and Buckland making Hobbits
Eagles' Eyrie making Eagles
Iron Hills making Dwarves
Entwood making Ents"