It wouldn't add that much time (depending on where your hotel is) to check into your hotel and dump your luggage in your room. Keikyu expresses will still be running in both directions.

There probably are lockers in Shinagawa station but they are most likely outside the turnstiles. The way the transfer normally works to/from Keikyu, you stay inside the ticketed area of JR to transfer, paying the Keikyu fare at a ticket window adjacent to the turnstiles connecting the two rail lines.

Note that the Narita Express takes an hour, not 30 minutes, to Tokyo station, and a bit longer to Shinagawa.