I don't think HDF5 has its own definition of a date/time type and you can't store MATLAB datetimes directly in HDF5. There are occasional references in the HDF5 documentation to a date and time type or "H5T_TIME", but it appears that it has not been fully implemented. I think the standard approach for HDF5 or netCDF files is to store times as an epoch (usually expressed in text) and a numeric offset. You'll want to choose your epoch and offset wisely to avoid floating point precision issues (e.g. if you've got microsecond-precision data, don't use "seconds since 0 CE" as your epoch). The datetime/convertTo method can help with the conversion from datetime.
This example illustrates some of the process of going the other direction (from HDF5 to MATLAB).
