Yes very sad, sometimes we do get these beautiful queens emerge from the cell but no wings, and sadly they will never mate.
It can be caused by mishandling of the queen cell, ie, if the larva is jiggled around when the wings are still being formed they can be damaged. But it is nearly always caused by DWV.
DWV can be transmitted by all the ways you say, but primarily by varroa mites. It is said that varroa mites do not go into queen cells but I know that isn't true because on several occasions when examining unused queen cells I have found varroa in the cell with the queen larva.
The photo clearly shows the wing deformity virus.. You have a very besmirched colony. The critical number of 2600-3000 ticks per colony. The virus is transmitted through ticks that parasitize in the cell, and bees infected with this virus can transmit this virus to the larvae along with food. Also, ticks that are not infected receive this virus through an infected larva.