I think it's safe to assume that any modern consumer electronics widget will have circuit fault protection. In fact even the $1 DC-to-DC converter modules under discussion have built-in thermal shutdown to protect again faults like a short circuit.
What makes your circuit "interesting" are the multiple long cable runs. That is, I can imagine a situation where you could have a short-circuit up on the shelf in one of the 6 circuits. But because of the resistance in the cable, the power supply down below does not "see" the short-circuit but instead sees some non-zero wire resistance and says to itself, "hey, no big deal, I'll just deliver more current" (to within its Amperage capability of course).
To your point, yes, if you can up the power supply voltage at the base, you need less current to deliver the same Watts (or Lumens of lighting) up on the shelf. So assuming we're going with Plan B (local regulation using the $1 converters), then I would absolutely go with a higher DC voltage...say 18V DC. Here you can dust off the textbooks and re-examine Ohm's Law and such but let's just say you'll be better off (more efficient) running lower currents.
An inexpensive way to gain some peace-of-mind would be to put a 25-cent resettable fuse on each circuit from panel to shelf. Like any "fuse" you need to choose its value based on the operating/fault current. Perhaps you recall some of the readings on your Volt/Amp meter when you had full lighting and windmill operation. I realize you now show about 5V and about 0.5 Amps. That's "only" 2.5 Watts (W = Volts x Amps) albeit with a portion of your real-estate empire in the dark.
So with no further analysis, and almost more to carry on a discussion, I'll draw an arbitrary line-in-the-sand and suggest targeting a max current per circuit to 1 Amp. If using 18V DC at the base, that's up to 18 Watts up the wire and depending on the wire length ~15 Watts available at the DC-to-DC converter. There is some power conversion loss when changing voltage levels but you'd easily have 10 Watts of 5V DC power. That will drive some 100 LEDs sections. Lots of hand-waving here but just trying to get arms around the problem.
If not familiar with resettable fuses, they are widely available and inexpensive. I found above using the sort-by-cheapest on eBay just to give you an idea. The key parameter is the so-called Hold current rating which in this case is 0.9A which is close enough to 1 Amp. In round numbers these devices will Trip at about double the Hold current...so at around 2 Amps it will open like a traditional fuse but is self-resetting so when you clear the fault it can live another day. Another parameter is the voltage rating in this case 72V...so 18V is well within its range.
Moving on. I'm not quite clear on exactly what you meant by having a timer trigger 15 minutes or whatever after turning on power. And then earlier you mentioned some kind of lamp timer-like device that came on at about 6pm every day or whatever.
In any case, I can recommend the above DC timer module if for no other reason than to start a discussion. I have used this module many times. One nice feature is it operates over a relatively wide voltage range ... so could be powered by 12V DC or 18V DC. Many timer modules are for 12V automotive applications and might have issues with 18V.
This module would be able to turn on or turn off after, say, 15 minutes. Or it has a cycling feature where it can turn on for X minutes, then turn off for Y minutes, and loop forever.
Here's a short video of this module in action I made for a different OGR train application. It's just to show the relative size of this widget.
So I can see one of these modules per circuit, placed in the base where you can access them as needed.
Then, suppose you placed a timer module on the shelf near buildings. This module could alternate between two different DC-to-DC converters to apply "full" voltage or "half voltage" to a set of buildings so they change brightness (in addition to going on/off).
Also, I like your use of the term "control" in the discussing timing. That is, once you "buy-in" to using these inexpensive electronic modules with Lego-like assembly, you might consider something like an optical trigger so that a timer module placed on the shelf triggers for some interval only when the train goes by.
