Using hardcoded *.pool.ntp.org servers in a default config of an OS is actually a violation of the NTP Pool project policies. It's just that when VyOS was a small project with few users, it didn't matter, and we definitely couldn't setup our own pool and offer it to NTP.org (or just use it ourselves).
Whether we are ever going to make a vendor pool at NTP.org or not, we'll have to replace old *.pool.ntp.org addresses with new ones.
When the new NTP infrastructure is in place, we need to add a migration script for it. It should only replace *.pool.ntp.org, custom user-defined NTP servers should be left untouched.