The reason is that they are at the bottom of the ocean and it is difficult to explore down there, it's much easier to look through a telescope at the stars. The team behind discovering them used radar satellites to detect the mountains presence under water; they reported their findings in Science Magazine.
What's different between this time using radar and previous times is the resolution has improved. In previous data-sets they could set everything taller than 2km, which shows about 5000 mountains in the ocean. With the new data-set they can see things taller than 1.5km which they believe means they can detect another 25,000 mountains on top of the 5,000 already discovered.
This data is important for how fisheries are managed and conservation efforts as wildlife tends to congregate around these mountain peaks. It also leads to better data on currents as the roughness of the seafloor helps direct which way currents flow. This leads to understanding how heat is transported around oceans and how it affects climate. It also can provide useful information for shipping which can use currents to support savings in fuel.