Update: You can now remove an App ID (as noted by @Guru in the comments).
In the past, this was not possible: I had the same problem, and the folks at Apple replied that they will leave all of the App ID you create associated to your login, to keep track of a sort of history related to your login.
It seems that they finally changed idea about.
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…