The use of the ~ operator instead of ! means, in my interpretation, that you take the 1's compliment of X and, if that is non-zero, then perform the assignment.
To my mind, the danger in using ~ is because of how C treats 0 as false, but anything non-zero as true.
Let's say X is 0x01 which C would treat as boolean true (as it is non-zero). !X would therefore be treated as false (because C would see this as 'not true'). However ~X would be 0xFE which C would also see as 'true'.
Therefore the expression you show will ONLY NOT be true when X is 0xff (assuming 8-bit values - extend as required for more bits), and would be clearer if written as:
if(x!=0xff) y=z;
Susan