Skulk refers to the power and toughness, not the base power and toughness. If it was referring to base P/T, your hydra would be considered a 0/0 and thus unblockable by a 4/4, but since it's P/T adjusted by +1/+1 counters and the like, it can still be blocked by a 2/2.
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"Life is a jape. Yours, mine, everyone's."
—Tyrion Lannister, A Dance with Dragons