Thanks all for feedback.
As per zeros not appearing, this is certainly a bug in 9.0.0 Mac. I have upgraded to 9.0.1 and now zeros are displayed.
As per the ticks, the approach was to use ChartLabels along with Placed.
BarChart3D[ Map[Labeled[#, Text[Style[#, Black, Opacity[1.], Bold, 20]], Above] &, {{1, 0, 2}, {0, 0, 2}, {2, 1, 0}, {0, 2, 1}}, {2}], ChartLayout -> "Grid", BarSpacing -> Large, ChartElements -> Graphics3D[Cylinder[]], ChartStyle -> Directive[Opacity[0.3]], AxesLabel -> {None, None, None}, Ticks -> {None, None, {0, 1, 2}}, ChartLabels -> {Placed[{"Osteo", "Ewing", "Rhabdo", "Neuro"}, Axis], {"Del", "Norm", "Amp"}}, ViewPoint -> {1.3`, -2.4`, 2.`}] which produces
Positioning of labels can be improved I imagine (on the Y axis, specially); but I have tried other approaches mentioned in SE here and don't seem to work for 3D graphics.
Using Ticks as I did before placed the labels much better :( although those odd looking positions are still puzzling me.
Could someone improve on this? :)