Some NPCs do not include merit, while others do. Those asking for GPA, test scores, etc. presumably do.
For need based aid they are more likely to be accurate for married parents (or widowed single parent) with mostly W-2 income and ordinary assets. For small business, self employment, farm, or rental income, some colleges treat related deductions unfavorably; some of their NPCs may be less accurate.
If the parents are divorced, see http://talk.collegeconfidential.com/financial-aid-scholarships/2083835-faq-divorced-parents-financial-aid-and-net-price-calculators.html .