See this link: http://aws.amazon.com/dynamodb/faqs/
1 Write = 1 Write per second for an item up to 1Kb in size.
1 Read = 2 Reads per second for an item up to 1Kb in size, or 1 per second if you required fully consistent results.
For example, if your items are 512 bytes and you need to read 100
items per second from your table, then you need to provision 100 units
of Read Capacity.
If your items are larger than 1KB in size, then you should calculate
the number of units of Read Capacity and Write Capacity that you need.
For example, if your items are 1.5KB and you want to do 100
reads/second, then you would need to provision 100 (read per second) x
2 (1.5KB rounded up to the nearest whole number) = 200 units of Read
Capacity.
Note that the required number of units of Read Capacity is determined
by the number of items being read per second, not the number of API
calls. For example, if you need to read 500 items per second from your
table, and if your items are 1KB or less, then you need 500 units of
Read Capacity. It doesn’t matter if you do 500 individual GetItem
calls or 50 BatchGetItem calls that each return 10 items.
The above applies to all the usual methods, GET, BATCH X & QUERY.
SCAN is a little different, they don't document exactly how they calculate the usage but they do offer the following:
The Scan API will iterate through your entire dataset and apply the
filter conditions to every row. Since only 1MB of data can be scanned
at a time, you may need to do multiple round trips (using a
continuation token) to complete the scan. Further, using this API may
consume much of your provisioned read throughput. Hence, this method
has limited scaling characteristics and we do not recommend that you
use it as a part of your application’s regular behavior.
So to answer your question directly: The calculation is made on what data is returned in all cases except for SCAN, where there isn't really any clear indication on how they charge. A query that yields no results will not cost you anything.
You can definitely set up a caching system infront of Dynamo, definitely recommend you look into that if you want to keep your reads down.
Hope that helps!