The vaccine study with the link to autism was proven to be fraud. The doctor that conducted it just made stuff up! He even made up patients. Everyting he has said was discounted and he was barred from ever practicing medicine again.
As for drug companies conducting the studies, legally they have to. It's the only way to get a drug, inculding a vaccine, on the market. Every care is taken to keep the studies blinded, which means no one knows who is getting drug vs placebo. So the doctor, company, and patient does not know if they are getting real vaccine or saline solution. It can be very difficult to determine what is or is not related. Coming from industry side, I can assure you that in the protocols we ask that EVERYTHING is reported. If the doctor blows it off and doesn't report, there isn't much we can do about it. Even if it is clearly not drug related- say someone stubbs their toe and breaks it- that should still be reported.
I just got my Hep A & B vaccines a few weeks ago because I will be traveling to Israel next month and there is a high rate of infection there. Apparently you can get it from other infected people or dirty water. They hurt like a son of a buscuit! Far worse than tetnus and ached for days. I wouldn't wish that on a newborn. I don't see why it couldn't wait until they were a bit older unless they were traveling internationally.