What's to say Nobodies didn't exist? Remember, MX tried to force Ventus to use the Darkness with Neoshadows in that one flashback, so the Heartless obviously existed. Thus, to some extension, there must've been Nobodies scattered around the worlds. They may not have been very active, but they were there. Also, the Nobody Symbol is, at its simplest, an upside-down version of the Mark Terra, Aqua, and Ventus have on their clothing. Apart from the armor itself, it could just be a clever reference to Xemnas. Nomura does all kinds of things with his characters. Also, it is in the Mirage Arena, so it could be a wide variety of non-canon reasons.
Let me know if I need to put the Flashback bit in a spoiler box.