In my opinion, it doesn't really matter. 16-bit is the same as is used by audio CDs. Unless you intend to always listen in a professional studio environment, it will not be possible to hear the difference between 16-bit and 24-bit.
The only difference between 16-bit and 24-bit is the level of the digital noise floor. For 16-bit, the digital noise floor is extremely low - typically much lower than other noise sources that will be present. For 24-bit, the digital noise floor is even lower.
One benefit of using 24-bit FLAC is that you never need to change the dither settings - just leave it set to "shaped" all of the time. The reason being, that dither noise for 24-bit is totally inaudible.