Advantages of Physical Flashcards:
The biggest advantage is the flexibility. You can create any learning system you want and are not constrained by the software limitations or design.
The act of making and writing them out is part of the study process, which does improve memorability. However, this is often overstressed as in reality the effect is only small since the cards are created only once.
Physical flashcards can be used as stickers around the house. For example, if you are learning a foreign language, you can stick the translations on the items you use, like on mirrors and fridges.