There is a bug when you try to delete a map with the API. Elements concerning this map are not deleted in the other maps.
In the file class.cmap.php, line 677, I think you have to change :
' WHERE '.DBcondition('sysmapid',$sysmapids).
' WHERE '.DBcondition('elementid',$sysmapids).
Thank you for the API. With python, it's a real pleasure to interface our system with zabbix.