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I know that it acquired that designation as being a mystery due to large numbers of ships disappearing, or in some case, found abandoned with no crew aboard and none of the lost crew ever reappeared. As planes came into being they too began disappearing.

As ship to shore communication became available, it furthered the mystery as these ships & planes not only disappeared they also sent out no distress communications.

Thus, ships & planes disappeared without any attempt to communicate their situation. Of course all mysteries have understandable answers, and as technology advances answers are explaining some of those disappearances as their discoveries are found and more information can be gleaned to solve the "mystery". Those that are still not found and identified, still remain a "mystery" due to the fact that no facts can be stated to dispel the "mystery".

One of the definitions of mystery is; Something secret or unexplainable; unknown.

So it depends on what you mean by the word mystery, for it has several meanings.

However, one explanation as to why ships & planes go missing, is the understanding that sunspot eruptions have been known to cause tools such as compasses to spin out of control, which would cause navigation to be imperiled. Another explanation is that storms seem capable of coming from nowhere to create dangerous conditions to take boats by surprise. in both old & current times.