Does it make a difference if both parents hold a destiny knot?
Solution 1:
No, both pokémon holding a destiny knot when breeding will have the same effect as when only one of them holds a destiny knot.
Solution 2:
No, it will have the same effect as using just one.
When breeding you usally want to pass down a Nature to the offspring, and you achieve that giving an Everstone to a parent. If you use two Destiny Knots you can't do that.