It does seen weird to give a vaccine in the scruff of the neck, but it won't be any less effective. As long as it gets into their blood stream they will develop immunities.

Core vaccines (which is typically feline herpesvirus, calicivirus (FCV), panleukopenia are usually given in the shoulder. They are made up of modified live viruses, rather than a killed virus. (Basically they take a virus and copy its genetics, but in such a way that it won't be harmful to the animal like the original virus was.) I think most of the reasoning behind doing it in the shoulder is in case of vaccine reactions. Sometimes they will get a little fluid bump for a few days after the injection, or sometimes hair loss or discoloration (this is called alopecia- unfortunately it is permanent, but not harmful). Soreness is pretty common too. Very rarely, a tumor can develop months or even years later. I think for your pets sake, its better to have a sore shoulder, or (heaven forbid) a tumor there, than in their neck.

Rabies vaccines are a little different. They are always a killed virus, because that is what the law requires. Killed virus vaccines run a higher risk of complications than modified live vaccines. Injection site tumors are far more common in rabies vaccines, but they are still very rare. Typically, vets give this in their right, rear leg (hip). Because reactions are so much more common with this vaccine vets are usually more religious about giving it in this specific area- that way if there is a weird reaction in that area they will automatically think about the vaccine being the cause.

As to frequency of vaccination- it will to a certain extent, depend upon your vet. Rabies are standardized- there is a 1 year form, or a 3 year form. For core vaccines some vets will recommend every year, some less frequently than that. My personal vet (who actually used to be the state vet- so you know he's not a quack) has always tailored to our animals specific needs. Indoor-only kitties have very low exposure risk, so they don't need boosters very often. In the case of my 15 year old cat (who has since pasted on at the age of 18), he recommended that at her age the risk of reaction to the vaccine was far greater than of her contracting anything, so we didn't vaccinate her at all.

Hope this helps!

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