NEX is designed to be used as a commuter train; that's why it makes additional stops between NRT and Tokyo at certain hours (inbound in the morning and outbound in the evening). The 8:50 am departure from NRT is the last inbound train that makes commuter stops.

They sell standing tickets on the NEX once all the seats have sold out (as mentioned in the automated announcements on board), so it is possible for it to get pretty crowded, though not nearly as crowded as a regular commuter train.