Mark, the ntp profile in Ubuntu supports the NTPD_DEVICE tunable and
after reading https://www.kernel.org/doc/Documentation/pps/pps.txt it
seems like this would be the appropriate place to put this. Eg

$ cat /etc/apparmor.d/tunables/ntpd
...
#Add your ntpd devices here eg. if you have a DCF clock
# @{NTPD_DEVICE}="/dev/ttyS1"
@{NTPD_DEVICE}="/dev/null"

Adjust that to be:
@{NTPD_DEVICE}="/dev/pps[0-9]*"

Then do:
sudo apparmor_parser -r /etc/apparmor.d/usr.sbin.ntpd

The above expands to the equivalent line you proposed in the
description.

Would this suit your needs?

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https://bugs.launchpad.net/bugs/1564832

Title:
  Apparmor profile for NTPd needs to allow read/write access to
  /dev/ppsX

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