Is it normal as a researcher publishing a new theory or model to keep having uncertainties and self doubt? Even if your theory or model has been proven by experimentation and accepted for publication... is it normal to still doubt oneself and have uncertainty in their proposed theory/model? 

Or does this mean there's really something wrong in the theory? 

EDIT: And what happens if one day you discover that your theory can be broken.. but, after you had already published it?
This means that you are proud about your work, and know that it is really a breakthrough. 

I too had these uncertainties when I was publishing a new model. This was the first time I felt that way even though this was my fifth paper. What I realised is that the previous work I published was not revolutionary in a way that would attract negative discussions and critics. I was simply confirming the theories of others. These were "safe" publications, the kind that would easily be accepted and cited, and could not affect my career. I believe science was build by "bold" contributions, and that the "safe" ones will eventually be forgotten.

Any theory will be broken, sooner or later. Do not worry about that. Insist on logic and rigour when writing your manuscript.