First things first! Buying Decks on a CD is illegal. The real Decks don't come in a CD format.
The Cd version has it's advantages and disadvantages.
Disadvantage = You have to sit in front of the computer to read. Now reading from the monitor does put some extra strain. You will need to reduce the brightness and contrast every time you sit down to read[ Not a big thing if you can store settings]. You might start using the computer for other things [read SDN! and games].
Advantages = Like you said, it's cheaper. In some versions, OCR [optical Character reader if I remember right] software has been used. What this means is that if you are studying Physiology and suddenly want to check out on Adrenal Medulla, just search for it and all the files with those words will open up. You don't have to worry about loosing a flash card. They are always sorted.
The choice is yours