Why are Arduino clones cheap?
All the factors mentioned in the question apply to make the cost so low.  However, with an exception or two as noted in the next paragraph, “low quality parts” is not much of a factor, as explained in two paragraphs after that.  

Possible low quality parts include the USB mini-B socket, crystals or resonators, and the reset switch.  The socket and switch contain metal shapes that can be well made or badly (and more cheaply) made.  Those badly made will function but may have shorter lives and higher failure rates.  For example, the USB cable fit may be loose, or the switch may fall apart.  Crystal or resonator accuracy and stability can be poor while still allowing a Nano clone to appear to function ok.

However, SMT (surface mount technology) or SMD (surface mount device) parts on the board cannot be made significantly more cheaply than can good parts.  SMD LEDs, resistors, diodes, voltage regulators, and capacitors come off of automated assembly lines with little or no manual intervention.  See, eg, ceramic capacitor manufacturing at wikipedia.  Parts are automatically packaged into sealed reels of parts suitable for use on an automatic pick-and-place machine that populates PCBs.  In short, the dozen 0603-size SMD LEDs, resistors, and caps, and the nine other passive or small-scale-integration SMD parts on the board will cost about the same coming off a bad manufacturing line as from a good line, so there is little profit to be made producing bad parts.  The 20-odd passive parts probably cost a couple of cents, at manufacturing scale.

Active SMD parts like voltage regulators, the ATmega328P, and the 32U4 or CH340, likewise come off automated manufacturing lines.  As these parts are more expensive, there is more economic incentive for cheating, and from time to time fake parts get sold and used.  In the past (and perhaps still) there have been manufactories that specialize in removing labeling on the tops of cheap or non-functional chips, and putting accurately detailed fake labels for expensive chips on instead. (For example, NCP5318 buck regulators relabeled as ATmega328s.)  In short, most of the active SMD parts on a Nano either are genuine and work or obvious fakes that don't work and earn their sellers bad reputations or jail.  

The CH340g USB-to-serial chip  vs. ATmega32U4 USB issue is more complicated.  Ie, some may think of the CH340 as a lower quality part than a 32U4.  The CH340 may need a different USB driver than the 32U4 and may not support 57600 BPS serial in some cases. 1, 2.  The ATmega32U4 seems to be available on Alibaba for $0.10 to $.20 in moderate quantities.  I think the CH340g is made only in China and is somewhat cheaper than the ATmega32U4, so its contribution to the BOM total cost may be a few cents.

The PCB probably costs 5 to 10 cents, and assembly is free except for amortized costs of pick and place machines and an IR reflow system with a conveyor.  Boards probably are processed (components placed and soldered automatically) in panels of several dozen units, tested automatically, and then separated for packaging.

Summary: Inexpensive parts and automated processing hold down the per-board costs, moreso than cutting corners on component quality.  Corners may get cut on assembly quality and on quality assurance inspections.