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Yes, structures and track get thorough inspection after any earthquake when there is the slightest possibility of there being an issue.  I am certain the Japanese have a thorough detailed program for this sort of thing.  Again, dealing with fault movement when you are on earthworks or structure is completely different from when you are underground.  Mitigation, or more anticipation of movement by having a larger cross section in the vicinity that allows for adjustment of the alignment without digging a new tunnel, at least if your guess is not exceeded, but whether the lining is  in segments or not is near insignificant.  It will be destroyed in the vicinity of the fault.  This is not the same as movement of the BART sunken tube across the bay, which by the way best I recall does not cross a fault line, but did move some in a quake.  Going off the rail or even off the structure or trackbed in total if you are outside is far less a disaster than doing so in a tunnel.