I pronounce them differently:
GWEN ith and GWIN eth. If I had to pick one I'd choose
Gwyneth, because
Gwyneth is a fairly ordinary name and
Gwenith is a very unusual variant. Also, it's too agricultural for me and makes me think of wheat gluten.
I think it's fine to use
Gwen as short for
Gwyneth.
Gwyn is a boy's name!