Electronic – Jumpers within diode through-holes in a PCB

Yes, you definitely need a diode that can withstand the full driver output voltage. The cathode will be boosted to Vcc above that voltage while the anode is held at Vcc.

The lower leakage of a non-Schottky diode will be an advantage, but the slower speed may affect the efficiency of the boost function. However, that part of the circuit usually has plenty of design margin, so it shouldn't be a big deal.

No, the holes through the board should be plated, which means that they are lined with metal that makes a good connection from front to back. In my experience, capillary action will suck the solder all the way through the holes anyway. However, it looks like you are planning to control some significant currents so you might want to make the traces that conduct large currents much fatter. I would also suggest adding a ceramic capacitor of 0.1uF or so right at the power pins of the microcontroller, in addition to the 22uF caps.