Obstacle abeam, say right of track - fix established to ensure aircraft passes safely over before turning right.
Using fly-by waypoint would have aircraft use turn anticipation and turn inside fix, compromising procedure as designed....
You're talking about a conditional waypoint, right? eg. reach 2500' or fix YADDA then proceed direct BLAHH. I don't think that has any relation to LNAV and navaid outtages, does it?
The FMC really doesn't care that the NDB isn't there. It knows how the waypoints are coded and where it should go next - navaid or no.
It seems that there's no logic to this, just how conservative your controlling agency, POI, etc is.