It's normally used to mean the mental anguish we put ourselves through, especially when waiting for important news (eg. exam results). You imagine yourself dying one hundred times. The common expression is "a coward dies a hundred deaths" (ie. a coward will imagine him/herself dying a hundred times), which is a misquote from Shakespeare's Julius Caesar: "Cowards die many times before their deaths; The valiant never taste of death but once."

Dying one particular way may or may not be painful. If one person dies in one hundred different ways, that will be very painful and their suffering would be unimaginable. I wish that you have a lot of pain and suffering.

It is sometimes a idiom meaning "to suffer" "I hope you die a thousand deaths!" (I hope you suffer.) Sometimes used in poems for the same meaning "to suffer".