It is not that Eva is unable to tell The Deweys apart, she simply thinks that there is no reason for them to have individuality.  The Deweys come to Eva's home on separate occasions, and each boy looks strikingly different from the other two.  Eva has taken on these boys because they are not cared for by their mothers or other family members.  When Hannah asks her mother how they are going to tell the boys apart if they all have the same name, Eva replies, "'What you need to tell them apart for?  They's all Deweys.'"  Because the boys abandon their given names, they take on the identity of Eva's home instead.  So the unwanted children find a new identity as members of a group:

"Slowly each boy came out of whatever cocoon he was in at the time his mother or somebody gave him away, and accepted Eva's view, becoming in fact as well as in name a dewey--joining with the other two to become a trinity with a plural name. . . inseparable, loving nothing and no one but themselves."

This is significant because the novel tackles issues of identity, and The Deweys suggest one aspect of the formation of identity.  They become one, and in the end, even die together on Shadrack's Suicide Day.