To me it seems strange that a word indicating a feminine person is neuter. So holka is feminine and děvče is neuter?
Is there any difference between holka and děvče?
Nope. Though HOLKA seems more colloquialn (yet it is a proper word) and is more common. Dívka and děvče, that both also mean a girl are little more formal. Děvče even sounds little archaic in some parts of CR.