Well, unfortunately the OED says the origin is unknown and:
It is uncertain whether there is any connection with the slightly earlier use of munter in Australia and New Zealand to denote a loutish individual.
Their first two quotations show it's originally UK student slang.
1999 A. Losowsky Let. 21 Apr. (O.E.D. Archive) , Words and phrases especially prevalent at Warwick [University]... Munter, ugly female.
2000 Journal (Newcastle) 8 Dec. 26/5 Student glossary... Ugly boys and girls: Munter, minger, mutt, biffer.
I found some earlier examples.
Mozza, uk.music.rave, June 1997:
In our circles here in deepest darkets Oxfordshire we also use the
word 'munter' to describe a person who is somewhat less than
attractive - eg 'that short fat bloke at the bar is a complete munter'
^^[-_-]^^, uk.music.rave, Dec 1998:
My friends from way back in the years at school used to use 'munter' to mean
an ugly person.
Ignacy Sawicki, uk.music.rave, Feb 1999:
In the local, Cambridge parlance 'munt' is the noun used
to describe a seriously unattractive female, as in 'She's a munt!'.
The Munter hitch named after Swiss mountain guide, Werner Munter, born 1941. My guess is they're unrelated.