L- LPF in the power filtering
Can L-filter be ever used (so easily) to filter power, and what are
  the best practices?


I pretty much always (when implementing an LC low pass filter to remove noise on power rails) design it as an RC LP filter and put the inductor in parallel with the resistance so that DC currents are supported by the very low impedance of the inductor (as opposed to passing through the series resistor and giving a bad volt-drop).

I choose the inductor value such that it does not produce significant (or chip-deadly) overshoot in the worst case scenario. The resistor in parallel with the inductor reduces Q to the appropriate level to avoid significant overshoot.


  Does the simulation show correct symptom for frying the device if
  connected to different power supply (or "unrestricted" USB port if
  such exists)?


Yes, I've blown up chips when a surge load current was disconnected and the LC produced ringing that destroyed devices that were intended to be "smoothed" by the LC.


  Am I correct supposing that circuit does not fry because USB port has
  current limitation?


You might be, but it is load current passing through the inductor that quickly terminates that I have found to be the main issue on my designs. A fast rising input supply can also cause this problem.

Design it as an RC circuit and regard the inductor in parallel with the resistor as a component that supports low DC volt drop.