Ubuntu using atomic clocks would surprise me. Sure they could, but it's not obvious to me why they would spend $$$$ on such. More plausible to me seems that they would be using GPSDO as reference clocks (in this context, about as good as your own atomic clock), iff they were running their own time servers. Google finds only that they are using servers from the NTP Pool Project, which will be using a variety of reference clocks.
If you have information on what they actually are using internally, please share.
If you have information on what they actually are using internally, please share.