Here's a wild ass guess as to a possible cause:
The Model 3 doesn't have "fuses", it has computer controlled switches (aka transistors) and current sensors. So it's possible the system is cutting power to the sub's amp, either due to an actual over current detection, or a software bug. Or possibly a mixture of both...at some point over current is detected and the power is cut, but it isn't turned back on until some other event (reboot, software update).
That could also explain why some have this issue (their choice of music and volume levels trips the "fuse"), and some don't.
Is there a way to tell if the sub's amplifier is getting power?