Hello i'm Mehdi from French support care, 1) You will have to pay a licence for each system who run at the same time, but if it's just a replication or something it's not neccesary. 2)You should protect your windows VM in priority, but you can also protect your linux host, it's up to you. 3) If you protect your linux host, all your windows vm will not be protected correctly because the product for linux is not build for this. so if you protect your host, you should know that eset don't support indepth analyse of vmdk files(can't read guest OS disk).
If you have more questions, you can contact us by this form (in french) : hxxp://support.athena-gs.fr/demande_de_support.php?editeur=eset or by email : support@eset-nod32.fr