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.
Thanks for your response. (I will accept your response, I just want a little more onfo.) I am pro-choice in general, but this is late in the term. The vet is saying the only option is to abort, I just want to know if that is true. (So I assume the vaccine was live.) Could these kittens be "okay"? Is it just a high risk, or would they definitely be severely challenged? I am almost certainly going to get the abortion. There are too many cats out there to bring in another litter, let alone one with severe brain damage. I just wanted a second opinion about the severity of the deformity.
I see no good reason why they should have vaccinated her before determining if she was pregnant. She is the only cat in our house, and we are keeping her inside, at least until she is spayed. They were told she could be recently pregnant. Mainly I'm just upset that the vet took such a risk, and did not bother to inform us. Couldn't they also have gotten her in for spaying asap, instead of waiting three weeks for more vaccinations while her now deformed kittens grow?
I'm just trying to make the best decision, and I'm not 100% sure I trust the judgement of this vet. (Actually the SPCA)