Stating that scanning a web application takes X time is almost impossible. Keeping that in mind, I can tell you some trends and data I have gathered during my time as a Web Application Scanning Subject Matter Expert.
Solutions that require seat licensing take a fairly long time to setup and complete because the scans are serial. These types of solutions often run about 80 to 100 assessments per year. If you wanted to ensure you completed 100 assessments in a 6 month timeframe you would need 3 trained personnel and 3 licenses, this would allow for vetting findings and creating reports.
Contrasting a per seat license model, Qualys uses a per application license model and allows for (in Enterprise licensing) unlimited resources for that same cost. Assuming a scan takes 24 hours, you can complete 100 serial scans in 100 days. Since we can run the scans very multi threaded, if they are externally facing apps, you can assume 30 minutes of setup per app and scan as many as you want. It is possible to scan 100 apps all at once and have the results 24 hours later or, put simply, you could scan 100 apps in 1 day.
I would say that given 2 or 3 resources 100 apps scanned in 2 weeks is completely possible with plenty of breathing room.
Please feel free to contact me if you have additional questions.
Director, Web Application Security
jkent AT Qualys DOT com
This is tremendously valuable, Thank you both for the question and answer.