A better error handling has been introduced since version 2.13.2. However, this does not remove the error message. It just makes the message readable.
The problem was that h5ls was not able to deal with soft links. I changed the code accordingly, such that h5ls, h5dump, and h5read are now able to deal with soft links in an appropriate way. The updates will be available in version 2.13.6 that will appear in about 1 day in the developmental version of bioconductor.