Silence removal from the audio
1) No, if you have a particularly low level in one of the FFT points it will indicate that you have low energy in that particular frequency, but you can have several other frequencies at the same time.

2) In theory yes, but in practice the numerical precision will make the resulting signal slightly different than the original one.

Note: before applying the FFT you'll need to decode the mp3 file in order to get the audio data.