The point is that, just because a different threat exists, it doesn't negate the need for a defense against another threat. A bulletproof vest is useless against a head shot or to protect someone's arms and legs. It's still a viable defense.

The idea of layered defense is that more than one system is deployed to counter different threats. No one system will be 100% effective (virtually nothing made by humans is), but the sum of the layers can result in a very high effectiveness. The layers are designed to complement one another, so the total is more than the sum of the parts.

Layered defenses for missiles can include shipborne systems (like have been tested successfully several times) on AEGIS-equipped cruisers and destroyers to detect and attack missiles during boost and terminal phases. ABL, for all it's limitations, can possibly work during the boost phase. Potential space-based interceptors could work in the mid-course phase, and ground-based missiles in the terminal phase. They'd be supported by space-based sensors like DSP and SBIRS (and perhaps Space Based Radar) and by ground-based radars and the SPY radars on ships. All of these systems work together to accomplish the mission.

To me, the biggest benefit of any form of missile defense is that it removes the ability of a marginal power (like North Korea) from using nuclear blackmail against us. Suppose North Korea actually builds a few missiles capable of hitting some American cities, then threatens to attack if we oppose their attack on South Korea. Would we be willing to risk an American city to save an ally? Even a limited missile defense can negate that form of blackmail.

Consider how history would've been different had the Israelis not taken out that Iraqi reactor in 1981. By the end of that decade, Saddam would've probably had nuclear weapons. Had he gone ahead and invaded Kuwait in 1990, would a coalition have come together to displace a nuclear power? Odds are, the answer is no.

Just because someone can put a warhead in a shipping container, it doesn't mean that someone else couldn't put one on a missile. We need to protect against both possibilities. That's why SWAT teams wear both body armor and helments - to protect against different threats.