Any area that is left unfilled in InDesign is transparent by definition. The white that you see is a simulation of the substrate, which in most cases is white paper. If the substrate the piece will be printed on is clear, any area you leave empty will be clear.
It's important to be aware that there is no such thing in the CMYK model as "white ink," so if your design includes opaque white you will have to specify that as a spot color and ensure you're in synch with the print provider as to how that will be set up in the artwork.
Talking directly with the printer is essential to verify what file format will work best for them and that you and they understand exactly what is expected as a final product.