I am very sorry to hear about this difficult situation. These situations are each handled individually with the pros and cons evaluated for each situation. I would say that it is not common practice to vaccinate pregnant queens. If vaccine benefits outweigh the risks - like in a distemper outbreak.
Here's what the 2006 AAFP Feline Vaccinations Guidelines say:
"Unless specifically stated on the label, vaccines are not evaluated by manufacturers for safe use in pregnant queens, and routine vaccination of pregnant cats should be avoided. However, the benefits of vaccinating a pregnant queen may outweigh the risks in some circumstances (eg, catteries with endemic URD). If vaccination is determined to be essential, use of killed agent vaccines may be preferable."
It is possible that your vet chose to use killed vaccines which are safe in pregnancy. Most clinics do not routinely carry these products but perhaps the spca does. If a modified-live vaccine was used there is certainly some possibility of abortion or birth defects.
I am not sure why your veterinarian did not discuss the situation with you - I certainly would have as well as give you options.
As to whether or not you decide to abort the kittens, that is a very emotional decision and I think it is essential to know if the queen was given safe or potentially harmful vaccines. Please let me know if this fully answers your questions.