onedreamer
Dragon
Just checked my current game and there is no yellow happy face next to the Spider Pen in the city I built it in. I had 3 other spiders I just let wander around and get killed when the big barb units came out because I knew they wouldn't be of any benefit to me since I already had one Spider Pen and the silk it gives.
You're making a little confusion. First off, there is only one animal pen, which is the spider pen. Other buildings you are referring to are cages. Think of zoo ? They are 2 totally different things and therefore work in a different way. Second, the spider pen does not give a happy face as you thought, but it provides one silk resource, which is treated like resources are normally treated. Also it's not true that if you already have silk, a spider pen would be useless, since the added silk resource can be traded away.
Lastly, I feel like suggesting that I never found Giant Spiders becoming obsolete. Since you can get them very early in the game, it's not uncommon for you to get Combat V, Mobility I, City Raider III. They are invisible to most units and with Nature's Revolt they can get a base strength of 5. This means that in the open they will be always useful, not to mention the harassment you can put up with them. For example in the early-mid game you can use them to weaken your neighbour's minor city defenses and help barbarians conquer them.