Check your keychain. After updating to Sierra to 10.12.1, I had over 500 copies one of my certificates, and a few others were duplicated a few hundred times.

I removed all the duplicates and kept just one of each, and my code signing time went from 30 seconds per framework down to about 1 second per.

I don't know how or why the certificates were duplicated, but the timing of the issue suggests it was due to updating Sierra.

2017-03-23 Update

You can skip installing the beta version of CocoaPods, because the COCOAPODS_PARALLEL_CODE_SIGN flag is also evaluated in the current release build.

Original Answer

Found an alternative solution, not best, but at least it's speeding up.It works (for me)

Cocoapods released a new beta version few days ago.

Which allows parallel code signing when running the embed framework script(https://github.com/CocoaPods/CocoaPods/pull/6088#issuecomment-257441733)

1. Install the latest beta version

gem install cocoapods --pre

2. Go to your Xcode target build settings and click the + icon at the top

3. Set COCOAPODS_PARALLEL_CODE_SIGN to true

And enjoy the increased building speed!

If keychain looks good, but problems exists – check the preferences and remove all duplicates in this file:~/Library/Preferences/com.apple.security.plist

For typical setup this file must contain only one record with login keychain reference.