How to identify a missing datastore for com.apple.securityd?
Resolution


  a. I have a crlcache.db reference that appears dead, but no number of deletion attempts makes it go away.


This was the root problem, but it was difficult to make it go away with any of the existing tools. The crlcache.db entry was ghosted in my Keychain Access application, so an entry still existed. While I had reset all of my passwords, I hadn't fully killed the Keychain. All the applications I listed were using the Keychain to find their information, hitting crlcache.db and then either retrying or throwing I had to manually remove both of these files (essentially a hard-reset of the entire Keychain):

~/Library/Preferences/com.apple.security.plist
/Library/Preferences/com.apple.security.plist


Diagnosis

It was very difficult to diagnose the issue because nothing would tell me which file did not exist. This comment, with its command that gathered bug information for Apple, was the most helpful. This produced a giant tar.gz with lots of diagnostic goodies that told me much more about what was going on. Make sure to run along with whatever application(s) is misbehaving at the time.

sudo sysdiagnose securityd


Among the many plain text debug output files it produced, there was a large one called fs_usage.txt, and when I opened it up, I could see 1000s of familiar entries 

08:01:11.999993  getattrlist                            /private/var                                                                                                                                                          0.000003   Twitter.3616
08:01:11.999996  getattrlist                            /private/var/db                                                                                                                                                       0.000003   Twitter.3616
08:01:11.999998  getattrlist                            /private/var/db/crls                                                                                                                                                  0.000003   Twitter.3616
08:01:12.000000  getattrlist            [  2]           /private/var/db/crls/crlcache.db                                                                                                                                      0.000002   Twitter.3616
08:01:12.000004  statfs64                               /private/var/db/crls      


Once I saw that, it was clear the Keychain was still the issue, and my ghosted entry had to go. Lacking the knowledge of how to perform laparoscopic surgery on the plist files, I simply amputated and started over.