When you cast an X spell, you declare the value of X and then pay for it.
So, if you want to counter a spell with CMC 3 using Disrupting Shoal, X = 3 and then the UU of the spell makes the total CMC = 5 total. Just because you exile a card with CMC 3 to pay for it without paying its mana cost doesn't change the actual mana cost.
In short, you will include the value of X when determining CMC of the Shoal spell.
So, if you want to counter a spell with CMC 3 using Disrupting Shoal, X = 3 and then the UU of the spell makes the total CMC = 5 total. Just because you exile a card with CMC 3 to pay for it without paying its mana cost doesn't change the actual mana cost.
In short, you will include the value of X when determining CMC of the Shoal spell.