As is reported in kern/38778, after some time of boot, ls -l /kern does not show anything.
The trigger to this symptom may be intensive files access, the number may be important. In my case, rsync -ah NFS/ to local-disk/ of large filesystem will easily trigger the one. In my case, the size is 180GB. But tar ztvf Large.tar.gz may be another example, someone told me. It only needs two minutes to make /kern empty.
I have looked at CVS repository and it turned out the changes between 2008/01/25 0000 JST to 2008/01/25 0600 JST is the reason to this behavior. See source changes in Jan. 2008
( cd /usr/src/sys ; cvs diff -D '2008-01-24 1500-UTC' -D '2008-01-24 2100-UTC' . )
may give you the related changes.
It is now reported to netbsd-bugs.

The responce to netbsd-bugs should be sent to gnats-bugs at netbsd.org. David Holland kindly transfered it, and it is now linked to the original -> KERN/38265