Well, Ditto can't breed with Ditto, so.. Ditto can't breed with other Ditto. I think you mean how they reproduce, and how there is so many. Here's my answer.
According to Bulbapedia, Ditto resembles an Amoeba, a single celled organism with no definite shape. If you have been through 7th Grade Life Science, then you should know that Amoebas reproduce asexually, meaning that the offspring only has one parent, and both are identical. Dittos could reproduce through Mitosis, Meiosis, and perhaps even Budding.
Bulbapedia also says that Ditto could be based on an undifferentiated body cell, which can change into a differentiated body cell just by sampling it.
Keep in mind that these are just theories, and you know what that means... They aren't official, meaning that Game Freak may or may not have intended it to be this way.
