Update.zip signing- different sha for the same file
Answered here as i wrote in the comment. The second hash is a SHA1 of the 3 lines in the manifest file.
I can obtain the second hash by running:
echo 'Name: system/lib/libcustom_jni.so\r\nSHA1-Digest: +PhV5XphkQTNTyM2TSRTeiaDlCA=\r\n\r' | sha1sum | cut -d\  -f1 | xxd -p -r | base64 
7ooFhqk1oYWF5pmVuSAhF2pFVNw=

The echo command adds the final \n so it must be removed from the command to not be duplicated.
Edit for posteriority:
The update.zip is then signed by SignApk using the -w argument, which makes it generate a ZIP comment, without which the installation fails.
The comment consists of signed by SignApk string followed by a signature block. Code at Android SignApk source
This was the last piece of the puzzle that allowed me to create a custom update.zip for my Prestigio tablet.