OP's post is more than 1 year old, so I guess it doesn't make a whole lot of sense debating his specific situation.cyt0plas said:She will need to be listed as non-accompanying, and examined for inadmissibility (background check, etc.). If she is not, she becomes ineligible for sponsorship. This is how people get in trouble - they don't list their spouses on the application, and then they get banned.
The ministerial instructions for express entry (http://www.cic.gc.ca/english/department/mi/express-entry.asp) state that the points depend on whether or not you have an accompanying spouse. If she's non-accompanying, your points will be your own, not the ones for both of you.
Be aware that there can be delays in processing, and that criminality can make her ineligible in situations where a Permanent Resident would not.
Just for the record and the benefit of Prats6:
It is fine to name your spouse in your application, but list her as non-accompanying. This is not misrepresentation, and it will not prevent you from sponsoring your spouse later. The upside is higher CRS points (potentially), but the downside is that the spouse has to go through family sponsorship which can take a long time.
In contrast, it is NOT fine to state that you are not married when in fact you are. This IS misrepresentation, and it is true that this situation means that the spouse can never be sponsored if the PA's application is approved.