Based on the information you have given, it looks like she derived citizenship in 1999, on the same date her mother naturalized. However, if her mother did not have full custody at that time, but only partial/joint custody, the old law has sometimes been interpreted in a strict way that would not give her citizenship at that time. If they interpret it that way, her citizenship would instead start on Feb 27, 2001, the effective date of the Child Citizenship Act of 2000.
In either case she became a citizen before turning 18, the difference is just with the time frame of the supporting evidence. Ideally she should submit evidence to satisfy both interpretations -- i.e. evidence of living in the US with her mother in 1999 on or after her mother's naturalization, and evidence of living with her mother in 2001 (or or after Feb 27). School records would probably be the easiest evidence to obtain (assuming the school still has those records).
As far as her trip to Cancun is concerned ... while it is important for your girlfriend to eventually obtain proper documentation of her citizenship, she doesn't need a US passport to go to Mexico and come back. Mexico will allow green card holders to enter without a visa, and the US will let her return with her green card. Although US citizens are supposed to use a US passport to enter the US, her US citizenship has not yet been confirmed by any US government agency, and there is a tiny possibility that she won't be recognized as a citizen, so she's still free to use the GC for travel.
But if the travel plan is for June 2013, that's more than enough time to get both the N-600 and US passport. The passport takes a few weeks, and the N-600 takes about 2-6 months. If she plans to get both, I would suggest getting the N-600 first in this case. There may be some complexities due to the old laws and custody issues, and the USCIS folks who deal with N-600 are more familiar with the old laws and complex situations than the passport authorities. Once the N-600 is approved, the US passport approval will be automatic but not vice versa. There would also be less paperwork when applying for the passport if the N-600 is approved first.