Are they counted as votes? That would mean the person at the top of the ballot have an advantage because of these donkey votes.

Yes, they are counted, because it is a perfectly valid vote.

This does indeed advantage the candidate who draws the top spot on the ballot (the positions are randomly assigned). In a preferential system it advantages the candidate in the final two that drew the higher position - it seems to be worth about 0.7% ( https://www.crikey.com.au/2010/08/02/whats-the-donkey-worth-... ).