Guide a beginner to setup a silent Water Cooling system

[Church]

• What do you think about the hardware I considered so far?
• Do you think the Swiftech MCP 350 / Laing DDC 3.1 is the most silent pump?
• What about the radiator? Would it be better to use two at different points in the loop or just one? With how many fans for one loop? 1, 2, 3, 4?

OK selection.
Maybe not the most silent, but good overall compromise in performance/silence.
Doesn't matter how they are/are not divided/where are placed in loop. Choose rads however they are simplier to mount in your case. As your hardware is rather cool as it is, no need for something more then 120x3. Maybe even 120x2 will suffice. For fans i advise scythe gentle typhoons.

• Would it be useful to cool some other components of the motherboard for overclocking purposes or the power supply unit for silence considering I don't want to afford more than one loop?
• What are the pros & cons of a system with no reservoir?
• What about the tubes, the fittings and their sizes? What tool should be used to cut a tube? How many fittings are needed? Should 90° fittings be used to shorten the overall tubing length?

No need to. Mostly thrown out money for bling purposes.
Cheaper, more compact. Harder/longer to fill/bleed.
Not much difference in flow/temps, so take smaller size, eg. 3/8"ID / 5/8"OD, will be easier to route tubing in your rather compact case. Pair or so of 90° fittings won't restrict flow too much. Just don't build using only such fittings.

• What should the coolant be composed of?
• What do you think about connecting the pump directly to the radiator? Where should the radiator go for an integrated system?
• Would it be possible to «refrigerate» the case in order to improve the transfer of heat?
• What precautions should be taken before and after the system has been set regarding cleaning & maintenance?

Best/simpliest/cheapest would be distilled water. Put somewhere in loop some silver kill coil or add pair of drops of some biocide to prevent algae growth and you should be fine.
Order of components in loop mostly doesn't matter, temps everywhere soon enough reach equilibrium differing in tenhs of degree. Route tubing however you find easier/shorter/simplier to. Except one rule - put reservoir before pump, as common liquid pumps are not self-priming (they don't suck, they pull water, and water from res should go to them by gravitation/self flow)
Of course extra fans/good airflow won't hurt, to not accumulate heat within.
Do not skip proper leak testing after assembling/filling loop before any powering on. You shouldn't have much issues with cleaning if you use plain distilled water instead of some dye premixes that can cause problems with residue/gunking. Check once few months for water level in res, and maybe add a bit if needed (water can veeery slowly evaporate a bit through walls of tubing).
Good luck.