Yes. Silencing is typically random early on in embryonic development and is then maintained in subsequent cells. So both X chromosomes are used, just not usually in the same cell, which is dependent on what the cell's predecessor used.
The paper described is interesting. It's a review, not a definitive result, but it describes some interesting hypotheses.
In one instance it's suggesting that there are several immune response-related genes that are in or near pseudoautosomal regions. These are parts of the X that don't get inactivated, presumably because they are similar to what is on the Y Chromosome. Sometimes genes near these regions can escape silencing and have some level of expression, so there's possibility that females overexpress some of these relative to males.
In another instance, it's suggesting that there could be negative selection against cells that contain more defective copies of these genes. As such, females would perhaps have an improved fitness over males due to a lifetime of selecting cells that are genetically more resilient to infection.
It's not an answer to the question, just possible suggestions that might explain a clear bias in the susceptibility.
