I have mixed Tetra/Prism and Hexa meshes in one domain. Now the partitions are unbalanced. Is that because of the hybrid character of the mesh?
Yes, this behaviour is normal for the default setting with hybrid meshes. This is because the partition weighting is vertex based and different element types have different control volumes.
When you put the meshes into separate domains, these domains will be handled separately. Since each mesh is homogenious (except for the prisms) then, the weighting will be balanced.
But you can also leave the mesh in one domain and set the expert parameter
part cvs weighting = t
This parameter can be used to enable a more complex, experimental algorithm for parallel partitioning. This method attempts to assign different weights to each node/vertex in the domain, depending on the complexity of the elements surrounding a vertex. It attempts to make a more balanced partitioning for mixed element grids.