While the Shinkansen is indeed fast and I have used it between Kyoto and Tokyo when I was terminating downtown, there is not a lot of luggage space on the Shinkansen. Also you would need to connect to another train in Tokyo to get to HND (which I have never tried) and I don't know how crowded or how much luggage space on the connecting train to HND. Going to NRT the Narita Express has plenty of luggage space but OP is going to HND.

I would not be concerned about not getting a Nozomi train if taking the Shinkansen because if you download a train schedule you can pick a Hikari train on the JR Pass that uses the same equipment but makes a couple of extra stops so it is still quite fast, just do not pick the slow Kodoma trains as those are much slower. The issue with the Shinkansen that always worried me was the lack of luggage space. I mitigated by traveling in non-peak seasons and hours and taking the Green cars. In Tokyo if going to HND I would worry about how crowded the connecting train would be in addition to how much luggage space there would be to HND, not an issue to NRT with the Narita Express since most folks do not use it for commuting and it has plenty of luggage space.

If luggage is not a consideration then, yes, Shinkansen is great. With check-in sized luggage the calculus becomes more involved.