Why does each fan blade have a different mass and frequency?
Because manufacturing processes are not perfect, and the minute differences between parts as-designed and as-produced are amplified by the high rotational speeds and large diameters of modern jet engines.

Take a following back-of-the-envelope calculation: disregard incoming airflow velocity and assume a hypothetical fan with a 1 meter diameter rotates at such rpm that the blade tip has a tangential velocity of 80% of the speed of sound at 35kft in ISA. The equivalent rpm would be 2817. 
$$
a_c=\frac{v^2}{r}=\frac{(295\cdot0.8)^2}{1}=55.7\cdot10^3 \; \mathrm{[m/s^2]} 
$$

That's the acceleration on the blade tip. If this blade were to be just 1 gram overweight, the force exerted on it would be:
$$
F_c=m\cdot a_c=0.001 \cdot 55.7\cdot10^3=55.7 \; \mathrm{[N]}
$$

that force is more than the weight of a 5kg dumbbell and it alternates its direction almost 3000 times per minute.

Its not that fan blades are hard to manufacture precisely, but that the application in which they are used is unusually demanding and any small imperfection in the blade will make itself known very loudly.



As for why the frequency is different, it is because the vibration modes of any system depend on the spatial mass distribution, like a pendulum which changes its natural frequency if you shorten the distance between the mass and the fulcrum. So the two issues you mention are directly related: a few milligrams of metal missing at the tip will shift the center of mass, and with it the natural frequencies of the blade.

In reality the whole vibration issue is a bit more complicated for continuous bodies, which effectively have infinite natural frequencies, because unlike ideal pendulums, their mass is distributed over infinite points in space, but that is a bit beyond the current point. 

The important part is not to have any natural frequency coincide with the rotational frequency of the fan, because that would quickly lead to rapid unplanned disassembly: the vibration amplitude would be amplified with each revolution until the blade failed.