After a few days of experimentation, this question should actually be split into two parts:
How do I properly use the Scan Hammer?
When you strike the ground with the Scan Hammer, it detects the mineral types directly under the point of impact. A box will pop up with the results of the scan, telling you what minerals a Thumper will extract from this point.
The Scan Hammer also sends seismic waves through the ground ahead of you, revealing mineral occurrence in the following colors:
Gray: Only traces
Yellow: Thumper nearby
Red: No Thumping
There are certain regions which tend to hold one type of mineral over another, but the best way to find out what's under your feet is to hop along, hammering as you go.
Why won't the percentage go much higher than 50%?
If you put down a Thumper on an "only traces" area, the only thing it will pull up is Sifted Earth (which can be processed at the molecular printer). If the Thumper is on top of a mineral deposit, a percentage of the haul will consist of the given mineral. For example, calling down a Stock Thumper on a spot with 50% Quartzite will return 500 Sifted Earth and 500 Quartzite on a full load.
Since Thumpers attract a significant number of bugs, you can also collect lots of Ferrite, Coralite, and other minerals as loot.