science/hdf5 by default doeesn't create any .pc for pkg-config to dynamically link with it's libraries. So far it seems we will need to use cmake.
I have just submitted PR 251894 which could solve this, if your port supports HDF5 1.12.0:
(In reply to Thierry Thomas from comment #1)
My problem is with science/py-netCDF4 which cannot find the library itself as there is no .pc file. Thanks for the patch. I will try to give it a shot once it lands in the tree.