I know this is a stupid question but do you have to put though dowels through a pre-stacked cake? (as well as the dowel in the centre).

For dummies? Nope. I just stick them together with piping gel, or I don't stick them at all. They are so light, they don't need support. If you're transporting them stacked, I'd use some piping gel or leave them unstacked until you get there.