This makes me think, does this change between renderers?
Polymost does some Z hacking to get around rendering order issues.
This happened in both classic and polymost.
I should clarify that this isn't just a rendering thing. It's not that it's invisible; it straight goes somewhere else. I can hear the explosion in the distance, and remaining in that spot will not hurt you.
Actually, i remember this weird bug was happening very often in v1.3D DOS version as well. At least more often than it does in source ports. Or maybe i just had more "luck" avoiding the bug in EDuke32 than in DOS version, I dunno.