How to identify the reference genome assembly used to create a .hic file?
Turns out HiC file does store such metadata.

straw tool from Aiden Lab contains a script (read_hic_header.py) that prints out the metadata from a given HiC file. Usage: read_hic_header.py &lt;hic file or URL&gt; [verbose]

In order to obtain the metadata in the form of a dictionary, one may consider using a function of the same tool that is currently available in my fork.

from straw import straw_module
straw_module.read_metadata(infile,verbose=False)

Args
    infile: str, path to the HiC file 
    verbose: bool, print the metadata if True else return the metadata
Returns
    metadata: dict, the metadata is returned if verbose is False. 
                Keys of the metadata: 
                HiC version, 
                Master index, 
                Genome ID (str), 
                Attribute dictionary (dict), 
                Chromosomes (dict), 
                chromosomes2length (dict), 
                Base pair-delimited resolutions (list), 
                Fragment-delimited resolutions (list).