First there are really two types of missile defense systems. Those that worry about ICBMs, and those that are "theater" defense.
The US Missile defense system that is costing so much money worries about the first class, i.e. missiles coming from thousands of miles away that are ballistic in nature. We have a limited number of shots for such a defense - and really we're worrying about bad actors like North Korea or perhaps Iran. These guys are going to have a limited capability to throw things at us. So a small number of shots is about right.
These systems can NOT defend against Russia - who can throw several hundred missiles our way.
The theater defense systems are things like the Patriot or the SM3 (I think) that the Navy carries. These have some ballistic defense roll - but their main job is to worry about shorter distance ballistic missiles or air-breathers like the Exocet that was used in the Falklands war. A Hypersonic missile is going to fall into this class and indeed I believe such systems would be out-classed by a Hypersonic weapon today.
Perhaps with the next generation Laser weapons there might be a chance to defend against multiple salvos - but those aren't fielded yet.