Back then was a 9 year old and 1 day boy allowed to do yebam to his dead brothers wife?
Yes. However, it's not considered "real" yibbum; any relations that they have until he reaches the age of majority (13 years old) don't change that status. (So if they don't have relations after he reaches that age, then dissolving this marriage requires both a get and chalitzah. On the other hand, if they are intimate after he reaches age 13, then the yibbum fully takes effect, and only a get is needed to end it.)
(Shulchan Aruch, Even HaEzer 167:2. Rambam, Laws of Yibbum and Chalitzah 1:16, seems to say that in the first case only chalitzah is needed.)
Thanks to @DoubleAA for pointing out my mistake in the previous version of this answer.