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, color-coded to the type of resource, with a height equivalent to the concentration.
There are certain regions which tend to hold one type of resource 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%?
The maximum concentration of a resource deposit varies from vein to vein. Veins change at a regular interval, but it is very likely that the vein you're currently attempting to scan tops out at 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 refined at the molecular printer). If the Thumper is on top of a resource deposit, a percentage of the haul will consist of the given resource. For example, calling down a Stock Personal Thumper on a spot with 50% Aluminum will return 125 Sifted Earth and 125 Aluminum on a full load. A full load also grants you a double resource bonus, so that topped off Stock Personal Thumper would actually net you 250 Sifted Earth and 250 Aluminum.
Since Thumpers attract a significant number of enemies, you can also collect lots of other resources, DNA, and parts as well.