Tap-tuning is an art (grounded in science) that is shrouded in mystery. While some luthiers tap-tune only by ear, computer-assisted tap tuning allows the luthier to actually see a computer-generated frequency spectrum graph when muting a specific spot on the plate (e.g., top or back). Computer-assisted tap tuning has only been possible for a few decades. Until very recently, it was too expensive for most luthiers, as the software required used to cost many thousands of dollars. Finding the correct spot to mute is way beyond our scope here.
There are known “ideal” fundamentals (i.e., note perceived by the human listener) for most general types and sizes of instruments, including bouzoukis. The fundamental measured by a frequency spectrum graph, among other things, is a proxy measure for flexibility/strength of the plate. The thinner the plate the lower the pitch of the fundamental, and more importantly, its propensity amplify string vibrations, especially the lower frequencies. Tap-tuning is an iterative cycle of tapping-recording-analyzing-thinning the plate. With this real-time information, the luthier can determine how close to too thin the top or back is getting. In any case, when taping produces an almost bell-like ring (to the luthier's ear), it is time to stop. Thinning the plate further can result in an instrument whose sound lacks focus or would be described as “muddy”.
Tap-tuning is NOT done on cheap factory instruments, as it is too time and expertise intensive. Factory instruments are, therefore, overbuilt so as to avoid any chance of plate breakage due to being too thin. Of course, with the cheapest instruments, tap-tuning is irrelevant, as you cannot (or should not anyway) thin plywood with a luthier’s palm plane.
Another thing that tap-tuning helps with is maximizing the output of harmonic overtones, thus making the sound richer and increasing the instrument’s sustain. An experienced luthier uses tap-tuning analysis to selectively reduce (by thinning and scalloping) the braces once they are installed in order to increase frequencies in the tap tone spectrum besides the fundamental (i.e., the harmonics).