How does one calculate the values of LF1&2 and C93?
tl; dr: The designers didn’t calculate anything really. They likely just followed another design.

The LF1/LF2 filter elements are ferrite beads. They suppress common-mode noise coming from the board. This helps the board pass EMC / EMI testing.

Ferrite beads are rated in impedance at a given frequency, rather than inductance. In this case, they chose a 220 ohm @ 100 MHz ("LF221") as a standard value for a high-current bead. In general, you choose as large an impedance as you can in the size ferrite you need for your rated current.

C93 is a bulk bypass capacitor. 100uF is a standard recommended value for USB endpoint bulk decoupling.