OK so with JR pass, it looks like taking NEX to Tokyo then to shin-Osaka will likely arrive between 11pm and midnight at Shin-Osaka station.
What does transportation look like around that time or later? Is it still possible to take subway to hotel or should I just book the holiday inn or courtyard at the station for the first night?
I would transfer at Shinagawa, because it's less crowded and much less confusing than Tokyo. If you are just doing a round trip from Narita to Osaka and back, I would also consider paying a little more for a round-trip Nozomi ticket, which is faster and has far more frequencies than the Hikari service available on the pass (trains every 10 minutes vs. every 30-60 minutes). You should be able to get to Osaka around 10pm that way, and would have flexibility to take a break in Shinagawa for dinner or a drink before getting on the long train ride.
You might also consider spending the first night at Tokyo or Shinagawa and then taking the 6 AM shinkansen to Osaka -- coming from North America you'll probably be waking up very early on the first couple of days anyway.