Perhaps no aspect of national defence is as poorly understood as ballistic missile defence. After North Korea’s shot over Japan last week with an intermediate-range ballistic missile, many people wanted to know why it wasn’t shot down. The answers may be disappointing – but hopefully they will also be enlightening.

Focus on missile defence capabilities will only increase after Pyongyang’s claims on Sunday that it had tested a hydrogen bomb that can be loaded on to an intercontinental ballistic missile.

The first and most fundamental issue to understand is that developing and operating ballistic missile defence, or BMD, is an extremely challenging undertaking. Some are better than others, but the resulting systems are inherently limited in their capabilities and roles.

Perhaps the most attractive sort of defences simply do not exist today, and quite probably never will. So-called boost-phase systems are designed to stop ballistic missiles early in flight, while their engines are still firing and they are ascending into the upper atmosphere and beyond. At times, the US has contemplated a global network of boost-phase interceptors that would whirl around the planet in low-Earth orbit, but the complexity and the economics of the idea are forbidding.

More recently, the US built a prototype “airborne laser” – a massive weapon built into a Boeing 747, designed to burn a hole through an ascending missile, destroying it early in flight. The programme was cancelled on grounds of cost, shortcomings in technology and lack of operational realism: the plane would have to linger dangerously close to enemy territory to have any shot at a missile, making it highly vulnerable to attack just before launch. Opponents could also simply avoid launches from coastal regions.

A panel organised by the National Academy of Sciences has looked at other options, focusing on the mid-course phase, when missiles – or the “re-entry vehicles” that carry warheads in many types of missiles – are passing through space.

The ensuing report was very critical of the existing mid-course system for US homeland defence, known as Ground-based Midcourse Defence, or GMD, which is based primarily in Alaska and is intended to stop attacks on North America and Hawaii from North Korea. The academy panel advocated the gradual replacement of GMD with a substantially new, upgraded system. Instead, Congress has continued to put resources into the incremental improvement of GMD, whose flight-tests cost hundreds of millions of dollars each and have worked only about half the time.

Why is GMD such a basket-case? Partly because of the extraordinary ambition of the concept

Why is GMD such a basket-case? Partly because of the extraordinary ambition of the concept, and partly because of the hasty nature of development and deployment. In the late 1990s, an expert panel warned of a pattern of deficiencies in American BMD programmes, driven by perceived urgency to achieve “early capability”.

These findings do seem to have influenced a number of American BMD programmes, which have proceeded in a more systematic and satisfactory manner over the intervening two decades. But GMD, the showcase system for US defence, has not.

The Pentagon’s own in-house authority on testing and evaluation has slammed GMD for its unreliability, potential vulnerability to attack or disruption, and an insufficient network of radars. A report issued by the Union of Concerned Scientists last year depicted a programme operating under minimal oversight from Congress, at great expense, and with disappointing results.

Most of the rest of the world’s existing BMD systems belong to a third category: terminal-phase defences. America’s Patriot and Aegis systems and its Russian and Chinese counterparts, as well as Israel’s Arrow system, THAAD, all involve interceptor missiles designed to catch attacking missiles as they descend through the atmosphere toward a target. (THAAD has some ability to intercept above the atmosphere.) The test records of this class of defences have become increasingly impressive.

Patriot, THAAD, and Aegis are precisely the defences that would be employed against North Korean missile attacks in the region. But by virtue of being terminal-phase defences, they protect relatively small areas, close to their own locations. Patriot is often classified as a “point defence”, and used to protect military bases. THAAD is an “area defence” with a longer reach; the US has deployed a THAAD unit to cover its Pacific island of Guam, and another to protect the southern half of South Korea, both of which play host to a number of important American military facilities.

Aegis, which is primarily a sea-based system, differs by virtue of its high degree of mobility. Patriot and THAAD can move by road or by transport aircraft if needed, but Aegis-equipped vessels sail around the region at all times. South Korea’s Aegis boats are equipped with SM-2 terminal-phase interceptors; their Japanese and American equivalents also carry SM-3 mid-course interceptors, enabling a “regional defence”.

So why didn’t an American or Japanese SM-3 take a shot at the North Korean missile that passed over Japan last week? There are two main possibilities. One possibility is that no Aegis vessel was in any position to stop the missile. When it sailed over the island nation, the missile was well into space, about 500km high. The second possibility is that there was simply no reason to make an attempt. By this point, it would have been clear to Japanese and American radar operators that the missile was headed for somewhere in the Pacific, over 1,000km beyond Japan.

In short, it’s not always possible to defend empty reaches of the ocean, and it’s not really desirable to try, either.

Until there is an actual war, of course, we can’t know how effective they would be. BMD is not a panacea. Even the best systems must break at some point, faced with multiple salvos of missiles, attacks on different trajectories, manoeuvring warheads and other advanced technologies, and limited numbers of interceptors. Against an increasingly capable opponent like North Korea, it is possible that defences would only buy some time for the US military and its allies at the start of an immensely destructive war.

• Joshua Pollack is the editor of the Nonproliferation Review and a senior research associate at Middlebury Institute of International Studies at Monterey, California