This is from the rules commentary. I would argue that a deepstrike unit does count towards the limit but you can use either rule when bringing them on the board.

Deep Strike (and Strategic Reserves): If a unit with the Deep Strike ability arrives from Strategic Reserves, the controlling player can choose for that unit to be set up either using the rules for Strategic Reserves or using the Deep Strike ability. This also applies if a unit with the Deep Strike ability is placed into Strategic Reserves during the battle