Hey everyone,
For the last couple of months (100+ flight hours) I have not seen a single audio crackle or stutter, so I believe I found a remedy: MainThread headroom.
The basic idea is that your setup has to consistently absorb performance hits from settings, addons, scenery streaming and server latency. If any of these push the MainThread into saturation, stutters of all kinds become unavoidable, and that can also include audio crackling.
I described one effective method here. However, that approach requires either very strong hardware or very small performance hits (lower settings, etc.).