The manual pages for shutdown and init have been updated to clarify how -t and -n work upstream. The new documentation will appear in sysvinit 2.92.
The behaviour here is expected (just poorly documented) since init waits the time specified OR ntil all children processes have terminated. The behaviour Dan was seeing was init waiting just until its processes had all signalled they were done. To enforce a longer wait you can call shutdown with the -n flag. - Jesse