Duplicate Apple ID Keys?
Note that my answer doesn't offer any technical explanation of why my answer works. Only empirical and anecdotal experiences.

Some people have encountered similar issues in one form or another (duplicated Apple IDs, Apple iMessage keys, Apple ID certificates). Apparently this seems to be a bug introduced in El Capitan update, which causes many keys and certificates to be, for some reason, multiplied over time.

Deleting them seems ok, as your device will request new ones as needed for your purposes. For my purpose, it's to speed up Xcode codesigning build time, and it works wonderfully.

Related thread on deleting:
https://forums.developer.apple.com/thread/67063

iMessage keys deleting:
https://stackoverflow.com/questions/36259684/why-are-there-so-many-imessage-signing-keys-in-the-private-key-section-of-keycha

People noticed this since El Capitan:
https://discussions.apple.com/thread/7353727?tstart=0