HDF5 datasets can have a null (empty), scalar (singleton), or simple (multidimensional) dataspace. Datasets with simple dataspace can have shape (1,). Some systems like Igor Pro can only write simple dataspaces (hdmf-dev/hdmf#80).
For a scalar spec, both a dataset with a scalar dataspace and one with a simple dataspace with shape (1,) are valid. See also hdmf-dev/hdmf#80 and hdmf-dev/hdmf#269. This should be documented in the storage documentation.