If your requirement is,
I want to use version control system with these files and possibly
apply steganography to conceal the existence of the files from
then of course GPG'ing single files only isn't enough. You should encrypt and maybe even plausibly-deny the whole partition with something like TrueCrypt. Does this make sense? Only you can tell.
Once the partition is encrypted and hidden, does it make sense to have the files encrypted one by one? This depends on how a hypothetical attacked might gain access to the system.
The first level of access would be partition access.
This may be gained through straight key recovery (e.g., rubber hose attack, post-it attack) for a standalone system; on a connected system, once you allowed partition access to access your disk, the partition could be readable to a number of services with access to and from the outside, and this access could be compromised.
In a scenario which your level of wariness makes look farfetched, you might have forgotten a network share with weak password. Once the disk is unlocked, the share would then allow access to the plaintext files.
This, I think, is the only scenario wherein double encryption makes sense. The lead pipe attack scenario would naturally imply that access to the second layer might be secured with another judicious application of the same pipe, unless you went to the extremes of supplying a dead-man or kamikaze access (e.g., the unlocking mechanism on the external 'undeniable' partition also triggers a background filling of the partition, thereby trashing the hidden partition) AND the attacker hadn't thought of doing a low-level backup copy of the encrypted medium. The combined likelihood of these two events makes this a dark horse, in my opinion.
A more likely variation of the remote access scenario is that you have the need to run some service on the system, you need this service to have read access to some files that must be kept on the encrypted partition, you can't move these files to a separate, expendable and maybe even unencrypted partition, AND this service has a security vulnerability of which you are unaware.
To protect against this possibility, I believe you have no recourse except to doubly encrypt the files. Of course the service can't have access to the same encrypted files with the same general key, or exploiting the service would secure secondary level access to everything: you will have to use two separate keys, and if the same files need to be access from within and outside the service, you'll have to maintain two separate copies - or use two separate keys from outside the service, i.e.:
INNER ACCESS (key1) ---> file1_1, file2_1 <--- SERVICE (key1)
INNER ACCESS (key2) ---> file3_2, file4_2
file1_1, file2_1 <--- SERVICE (key1)
INNER ACCESS (key2) ---> file1_2, file2_2,
However, this all depends on your situation. There's no one-size-fits-all guideline that I know of...