Hello, if you allow me:
1. The application will be able to categorize and automatically filter information base on demand.
Ok. For this I recommend a webpage user interface to filter and a simple XML service to access henceforth with another programs you develop.
2. We want access to the database to be limited and only accessible with passwords for Security reasons
Of course, it's possible using the role attribute in your Wordpress to grant access permissions to the users you want, it's the solution more easy, but I could put a simple user/password form to access too (if needed).
3. We want the app to be linked with our wp site, such that data filled on line will be automatically added and sorted on the database
Of course, from any source you want, this is basic.
4. We will prefer the layout be compatible with Microsoft excel when there is need for export of files
I can put a button to download the excel with the info you want.
5. It should be such that selected files can be exported independent of other data
I can put a form with different options to export if you want
6. the application should be usable online and offline
I can develop a desktop application that downloads all the info from the database if you have internet and use the file downloaded if you are offline. Will require some maintenance in the future and the user interface need some changes but it's possible if you want.