ChickenLittle, 

I've only seen this episode the one time, and that was on its premier air date in 1995, and still remember Sharon Lawrence as Amelia Earhart displaying consternation at being told her "top secret mission" to surveil the Japanese military was common knowledge in the 24th century. 

One day I'll make it a point to watch it again just to see how accurate my recall really is. 

It should be noted that in 1995, abduction by space aliens was a bigger concern among some of the general public than it remains today, hence incorporating the idea into the Amelia Earhart mythos is not at all surprising by Star Trek:  Voyager story writers.  And, if no trace of her or her Lockheed Electra are ever found, then heck, maybe abduction by hostile space aliens is as good a hypothesis as any.