carrz said:
Dependance on "system of units" does not explain how did permittivity and permeability become a part of any equation in the first place, nor it explains why would this equation be true:
Yes, it does, although many people go through many courses in physics before they understand units and systems of units sufficiently to understand why. I will try to help as best as I can, but in the end there is no substitute for actually working a number of problems with different sets of units, like Gaussian, English, SI, Planck, and Geometrized units.
Suppose that you have some arbitrary (correct) physics equation a=b. Now, it is possible, in general, to use a system of units such that a and b have the same units. Such a system of units is called "consistent" with that equation. For example, SI units are consistent with Newton's second law: ∑f=ma where f is in Newtons, m is in kilograms, and a is in m/s^2.
However, it is also possible to use other systems of units which are not dimensionally consistent with a given equation. In those systems of units you need to change the equation to a=kb, where k is a constant which changes the units on the right to match the units on the left. For example, you could express Newton's second law in US customary units as: ∑f=kma where f is in pounds-force, m is in avoirdupois pounds, a is in ft/s^2 and k is the constant 32.17 lbf s^2/(ft lbm).
The constant k is present only because of the system of units and is the factor that is required to convert the units on the left to the units on the right. Now, a given system of units may have several such conversion factors. Any combination of those conversion factors with the same base units is also itself a conversion factor and will therefore necessarily have the same units and the same value.
So, in SI units, c is the conversion factor between m and s (SI units are inconsistent with E=mc^2), μ0 is the conversion factor between kg m and s^2 A^2 (SI units are inconsistent with Ampere's law), and ε0 is the conversion between s^4 A^2 and kg m^3 (SI units are inconsistent with Coulomb's law). So 1/√(μ0 ε0) is an SI conversion factor between m and s, and must therefore match all other SI conversion factors between m and s, therefore it must equal c.