If your ~/.gnupg/ ever had a secret key generated or imported with gpg1/gpg2.0 (which was the default for most distributions since very recently -- for Debian since a month ago). --delete-secret-key will delete only the 2.1 copy, leaving the key on the disk. Even worse, querying via --list-secret-keys will confirm that the key was deleted.
This means that if the disk is ever accessed by a third party (goons at a border, imaging or seizure, you sharing the machine, etc), the supposedly deleted key can be read.
As I understand, the code to manage secring.gpg has been ripped out of gpg2.1, thus cleanly removing the key would be non-trivial. Thus, a proposed solution would be to ask the user to delete secring.gpg in its entirety when a key is being deleted (its unlikely to be useful anymore), and/or provide an adequately dire sounding warning (you can use a patch I've once sent to btrfs as an inspiration wrt appropriate presentation).
There's currently a remark in a dark corner of README/migration that "The old secring.gpg is kept for use by older versions of gpg.", but 1. not many read such docs, 2. the wording doesn't mention that this keeping includes --delete-secret-key and that gpg will lie that the key has been deleted.
Users that have deleted a secret key in the past need to be warned somehow as well.