I have no idea how you battery is wired up etc but i would suggest that in a 16AH configuration that it is running multiple cells in Parallel and based upon that alone the amperage to supply 1000 W at 48 Volts is 1000/48 = 20 Amps. I think youll find that 20Amps wouldnt even make the batteries stress at all.
You worry way to much about stuff. Just build it get it running and start enjoying it.
1000W of power is nothing, you can pedal it with that much power with your feet. A human can produce some serious power its just for small bursts. Isnt it something like So it will all be good on your bike.
Elite track sprinters are able to attain an instantaneous maximum output of around 2,000 watts, or in excess of 25 W/kg; elite road cyclists may produce 1,600 to 1,700 watts as an instantaneous maximum in their burst to the finish line at the end of a five-hour long road race.
So get off you bum plug it all together on the bike adn show us a picture of the thing put together and your grin of riding it.