What is the point of these components on the schematic? (Digispark ATtiny85)
For the capacitors, see Bimpelrekkie's answer.

Zener diodes D1 and D2 reduce the usb data lines to USB high of 3.6V.

Diode D3 prevents USB 5V transients or overvoltage from damaging the 5V regulator chip V1 or the rest of the components. The device does not appear to be just a USB device. It also has it's own power input for standalone operation. The diode exists to protect that power supply, and everything else on the board when it is plugged into USB. The USB specification has a higher limit of 5.25V, so could potentially damage the 5V on-board regulator. I would guess that putting a diode at the USB port to protect the USB chip would be the job of the PC designer. Either way, the 5V connection to USB itself can be removed with no ill effects and then the diode would not be required. This is because the data lines are ground referenced.