I think you are being quite harsh, net labels are fine for embedded/digital stuff, which generally consists of quite separate functional blocks with few, easily reasoned signals between them (e.g. power + I2C). A lot of Sparkfun's products fall into this category.
If you look at say laptop or SoC development board schematics, they are full of net names, and they certainly aren't using physical pin positions. In fact quite the opposite, one physical device is often split into multiple schematic symbols (e.g. supply rails are one symbol). For the overall system, they use a block diagram or hierarchical schematic. Here is the BeagleBone schematic, which I think makes good use of net labels, e.g. the BAT connection on page 2: https://beagleboard.org/static/beaglebone/BEAGLEBONE_SCHEM_A...
I will agree with you on net names for analog systems, such as audio amplifiers or complex power supplies. There, net names can quite often be misused, as you need to keep more connections in your head when trying to understand a circuit, and it is much harder to remember all the net names than see a direct connection.
As I said, net labels are like GOTO. There are very specific situations where GOTO (or net labels) are useful.
They're also used in lots and LOTS of other situations where they're actively harmful.
Contexts like spark-fun designs, where the layout is almost always only one page is a situation where they're actively harmful.
------
I've done large, complex system designs without using net-labels at all. It takes a lot of thought about how to structure your component symbols, and was considerably helped by my EDA tool (Altium) having a facility to bundle multiple logically associated but non-bus wires into a single logical connection ("signal harnesses" - they're great), as well as very robust hierarchical design facilities.
It's absolutely possible to do, and you wind up with a much nicer schematic in the end, but it does take longer.
On the other hand, a site like spark-fun in particular sells educational components. The fact that they don't have decent schematics is really extremely disappointing.
The Arduino Uno by contrast uses routing too much in my opinion, and is quite hideous: https://www.arduino.cc/en/uploads/Main/arduino-uno-schematic...
If you look at say laptop or SoC development board schematics, they are full of net names, and they certainly aren't using physical pin positions. In fact quite the opposite, one physical device is often split into multiple schematic symbols (e.g. supply rails are one symbol). For the overall system, they use a block diagram or hierarchical schematic. Here is the BeagleBone schematic, which I think makes good use of net labels, e.g. the BAT connection on page 2: https://beagleboard.org/static/beaglebone/BEAGLEBONE_SCHEM_A...
I will agree with you on net names for analog systems, such as audio amplifiers or complex power supplies. There, net names can quite often be misused, as you need to keep more connections in your head when trying to understand a circuit, and it is much harder to remember all the net names than see a direct connection.