Single message conversion. MHonArc can be used to convert a message to HTML independent of archive processing. Hence, MHonArc can be used as general MIME decoder. There are pros and cons of both languages. In sum, Perl allows for easier modification, portability, and extensiblility.
C provides better execution speed.
There are other differences, so consult the documentation of both programs to get a more complete list. Your needs willl ultimately decide which program is best for you. For some time, there was a lack of development on Hypermail. However, there is currently a maintainer. With MHonArc, you have complete control on how your archive looks and feel, and operates.