I'll give you the standard answer:
it depends. :)
If you are storing single bits of data (a string, an integer, etc) for reuse in other tests within the same project, I don't see any reason why you could not use the Project and Project Suite variables. For that matter, if you create a variable of the type "db Table", you can link your Excel sheets, text files, etc, to that variable for being able to read that information into your tests. The caveat to that is that the db Table variable type allows only read-only access to the linked files. You can't then write out to the Excel or Text files.
If you need both read/write access to your files, then yes, you shouldn't be using the project and project suite variables. But if you are doing read only access, then there shouldn't be a problem.
Generally speaking, there is no direct advantage or disadvantage on using test complete's variables. It all comes down to your specific needs and usage as to whether they will provide what you need in the most efficient manner.
