Are there secure mechanical cryptosystems in use today? Not necessarily alphabetic either, ie digital but mechanical?
While we obviously don't know who is using what and where, we know the U.S. phased out their last mechanical systems (the KL-7) in the 1980s. The M-94 (Jefferson Cipher Disk) was a clever and simple implementation of a polyalphabetic substitution cipher, so there's no reason it couldn't be used today. But the U.S. Army stopped issuing them during WW-II.
Note that none of the known mechanical cipher machines would stand up to the kind of brute force cryptanalytic attack available on today's personal computers.
A cryptanalysis of the M-209 (Hagelin machine) written by Dennis Ritchie, James Reeds, and Robert Morris, went unpublished in 1978 as they were informed by the NSA that the principles of their attack were still in use in cryptosystems of the day. Dennis Ritchie still isn't publishing it.