Having an atomic clock behind your NTP server doesn't really gain you anything unless GPS is lost for an extended period of time. As long as a timeserver has a GPS lock, it's going to be disciplining the atomic clock the same way any other clock is disciplined, so you don't really gain anything. Even a cheapie timekeeping GPS chip can get down into the < 500ns accuracy range (and the Thunderbolt on my desk will get down to < 50ns).
(You can gain a little accuracy if your timeserver itself is running its main clock (the one that drives the CPU and all the busses) off of a precision frequency reference, be it GPSDO or atomic clock, but that's a separate discussion)
Oh, and if you're using NTP and not directly connected to a precision timesource (not over the network), you may as well give up on that level of precision anyhow. For that you need PTP.