The MongoDB documentation suggests that the MongoDB service should just be shut down via the Windows Service Control Manager:

net stop MongoDB

When I did this recently, the following was logged and I ended up with a non-zero byte mongod.lock file on disk. (I used the --repair option to fix this but it turns out this probably wasn't necessary as I had journalling enabled.)

Thu Nov 21 11:08:12.011 [serviceShutdown] got SERVICE_CONTROL_STOP request from Windows Service Control Manager, will terminate after current cmd ends
Thu Nov 21 11:08:12.043 [serviceShutdown] now exiting
Thu Nov 21 11:08:12.043 dbexit:
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: going to close listening sockets...
Thu Nov 21 11:08:12.043 [serviceShutdown] closing listening socket: 1492
Thu Nov 21 11:08:12.043 [serviceShutdown] closing listening socket: 1500
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: going to flush diaglog...
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: going to close sockets...
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: waiting for fs preallocator...
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: lock for final commit...
Thu Nov 21 11:08:12.043 [serviceShutdown] shutdown: final commit...
Thu Nov 21 11:08:12.043 [conn1333] end connection 127.0.0.1:51612 (18 connections now open)
Thu Nov 21 11:08:12.043 [conn1331] end connection 127.0.0.1:51610 (18 connections now open)
...snip...
Thu Nov 21 11:08:12.043 [conn1322] end connection 10.1.2.212:53303 (17 connections now open)
Thu Nov 21 11:08:12.043 [conn1337] end connection 127.0.0.1:51620 (18 connections now open)
Thu Nov 21 11:08:12.839 [serviceShutdown] shutdown: closing all files...
Thu Nov 21 11:08:14.683 [serviceShutdown] Progress: 5/163 3% (File Closing Progress)
Thu Nov 21 11:08:16.012 [serviceShutdown] Progress: 6/163 3% (File Closing Progress)
...snip...
Thu Nov 21 11:08:52.030 [serviceShutdown] Progress: 143/163 87% (File Closing Progress)
Thu Nov 21 11:08:54.092 [serviceShutdown] Progress: 153/163 93% (File Closing Progress)
Thu Nov 21 11:08:55.405 [serviceShutdown] closeAllFiles() finished
Thu Nov 21 11:08:55.405 [serviceShutdown] journalCleanup...
Thu Nov 21 11:08:55.405 [serviceShutdown] removeJournalFiles
Thu Nov 21 11:09:05.578 [DataFileSync] ERROR: Client::shutdown not called: DataFileSync