An alignment percentage of 40–50% is fairly typical for Hi-C data. Several factors contribute to this, including the fact that Hi-C libraries contain a sizable fraction of chimeric reads resulting from ligation events between distant genomic regions. Also, random ligation artifacts (e.g., misligated fragments) can reduce the number of valid alignments. For more details, you can see this (now classic) review: Lajoie, Dekker, and Kaplan, The Hitchhiker's guide to Hi-C analysis: practical guidelines, Methods 2015 (PMID: 25448293).