AWS DynamoDB Cost efficiency

I think DynamoDB isn't the right choice. As you said yourself:

DynamoDB bill depends on the throughput. 10 sec is not the point, let's say we can wait a whole minute.

DynamoDB is built for high throughput low latency. So the core feature of this Database is providing answers within single digit milliseconds. As you already figured out you pay per second which means if you don't need nearly the same amount (within the ability of scaling up and down) of reads/writes over a period of multiple hours DynamoDB is expensive as you pay for queries you don't need.

Our application executes a query which returns about 100k rows several times a day.

So AWS RDS seems to be more suitable for your case.