So what's your take on this? Is it really possible to create a complex filter just by manipulating the wires and the specific conductive metals used in the cable or plugs? What is really going on here?
The answer to your question is "yes it is" but it "depends".
This is going to get technical so hang on. The first thing you must understand is that it makes a difference if an instrument is passive or active. Active instruments almost always have a low impedance cable driver designed to overwhelm cable characteristics specifically so a cable WON'T change the sound. But even so if your cable is VERY long it still can make a difference.
Passive instruments are a whole nother ball game. First understand that the usual idea is that a cable is just some kind of magic conduit that carries the sound of your instrument from the guitar to the amp. But this is not the case. A cable is actually an electronic circuit that ALSO trys to carry to signal from the guitar to the amp without changing it (much). Understanding a cable as an electronic component you need to remember that a cable has not only capacitance (usually rated as so much per foot) but also inductance (has to do with how thin the center conductor is) and resistance (also depends upon the thickness and material of the center conductor).
In a passive instrument the impedance of the instrument is very high. The input impedance of the amp is usually very high as well. If we multiply the cable capacitance per foot by the length we in essence can figure out what value capacitor the cable represents. If the value is high enough it's just identical to adding a varitone to your axe. Yes, long cables will change the tone. Yes, cables have different capacitances. So one would think that the obvious answer is to use low capacitance cable. Well that might be true, but you can find that certain ultra low capacitance cables tend to be very microphonic. In other words if you tap on the cable you can hear it in your speakers! So there is much more to this than it might seem.
And there is more. The pickups in a bass or guitar are wound with lots of wire that makes for a high inductance. If we slap a capacitance (from the cable and the coil itself) on there, we can create a tuned circuit. The frequency of that circuit depends on L (the pickup) R (the volume control) and C (tone and cable capacitance). Depending on the various values of these parts you can have all manner of tone shaping. It can be from a mid-high peak to a high end roll off. So clearly the capacitance and the inductance and the resistance of the cable can dramatically affect the sound because of these effects. Even the connectors can add resistance that can change the tone. Personally I always prefer gold plated connectors because they always seem to be nice low resistance and don't corrode as fast so as to not get crackly for a very long time.
So now if you get to the question "are boutique cables worth the money?" you can only answer "yes" if the tone they give ON YOUR SETUP is one you are in love with. You just have to try these things. Who knows even some cheap crap cable might give that tone you want. Of course there are other considerations. Some are mechanical. I've mentioned microphonics. Others have to do with shielding efficiency. No most cables do NOT provide 100% shielding from hum. They usually have ratings for this. Cheap cables often don't have strong connections or hold the cable in the connectors so they break after a time or the wires come loose. Cheap cables will even have plugs that are not to common size specifications which may not properly fit in the jacks causing problems.
In short you may think cables don't matter but they do make a difference. Happily for reasonably short cables the difference in sound is minor and most people don't bother with it. But it is true.