Yes, we decided to go with train now. Realized that it would be more convenient.
We have flight at 21:15 from HND. Planning to take 15:00 train from Kyoto.

You get reguar shinkansen tickets with reserved seat and make to platform too late and you miss the train. You have two options. You can simply wait for the next train and board an unreserved car. Your fare ticket (fare and supplement/surcharge) is still good and you can uae it on Nozomi or Hikari shinkansen. They are frequent. The other option is to go back and buy a reserved seat for a later train, if one is available. You can do this on the train side of the ticket gate (i.e. don't exit the gate) maybe at the staffed window at the gate or maybe there is a reserved seat counter on the inside.

If you get a discounted ticket make sure of the conditions of use. It would be for a specific train and it might require you to exit the gate at the destination station within a certain time period after the arrival of the train you were ticketed on. Am not at all sure about this.

The Shinkansen from Kyoto to Shinagawa should take about 2 hours and 15 minutes. There is a Keikyu train to HND about 3/ hour during the day and it takes about 15 minutes. You should make it to HND about 1800. Note however that I have never taken the train to HND as I taxi but have considered it. I always stay in the city of my international return flight the night before just to be sure nothing goes wrong. You should be fine.

Actually I have taken that train but many many years ago before I could afford a taxi.