Can all Arduino Due pins be used as digital input/output?
Bear in mind that this has nothing to do with "Electrical Engineering".
This simply is an arduino question. And should be asked on arduino Stack Exchange.

Yes.

They can be used as input/output pins. [Simple 'tutorial']
If that even isn't enough or not working on your type of arduino, you can use I/O expanders or shift registers. 
Check them out on the internet. [I/O expanders]