A note, the situation you are describing only happens when the character subject to the super stealth CE is within 6 of the attacker. Why this is important is that the "super stealth" CE's all apply to characters with Stealth. So they don't count as the nearest enemy only when they have cover and are further than 6 squares.

Cloaked is different. When a character has cover, they are never the nearest enemy. Because the "superstealth" CE's don't cover that issue, it is left to Stealth, which can lead to the "untargetable" situations.

Remember, the targetting rules are that you can target someone in cover, ONLY if they are the nearest enemy, not "target the nearest enemy in cover".

Stealth: If this character has cover, it does not count as the nearest enemy for choosing targets if the attacker is
more than 6 squares away. A character can attack an enemy with cover only if that enemy is the nearest. If this
character would be the nearest enemy, the next-nearest enemy counts as the nearest instead. Follow the normal
rules for cover if the character with Stealth is within 6 squares of the attacker.

Cloaked: If this character has cover, nonadjacent enemies cannot target it and do not treat it as the nearest enemy when choosing targets. Thus, Accurate Shot cannot target this character if it has cover. A character with Sniper can target this character if the only intervening cover is provided by other characters, which the Sniper ability ignores.

Superstealth CE: Characters in your squad with Stealth (including this character) and who have cover cannot be targeted by nonadjacent enemies.

As you notice, the Superstealth CE lacks the bolded portion of the Cloaked defination. Since all the superstealth CE's are dependent on Stealth, they depend on Stealth for the bolded portions to pass on who is the next nearest enemy. Sadly, when the attacker is within 6, Stealth is negated, including the bolded portion. Thus, they can be the nearest enemy but still not targettable.