If you are serious about hundreds of inputs and outputs, if you have the skills, you would be better off designing a board rather than trying to buy one. A commercial product would be rather expensive. On the other hand, if you are just wanting to throw green stuff at the problem, you should look at Data Acquisition Cards, also known as DAQs. I have not seen one for the number of pins that you will need, but it has been a while since I looked. In a former life, I used to require something very similar, but I would design them for the specific application and I also had a corporation footing the bill. Depending on what this board connects to, you could significantly reduce your pin count and cost if you were to go with virtual switches on a monitor and toggle them with the mouse. On the output side, there are also some interesting options rather than using hundreds of I/O pins, but they also add complexity to the system.
If you want to reach for the stars, you better have long arms!