Have you tried cleaning with a good soap and then letting them dry? Something like Murphy's Oil soap or Pinesol.
My life jackets don't smell that good, so I wouldn't worry about putting them in the hatch compartments.
Worse comes to worse, you can put clothes in stuff sacks before putting them in the compartments.
Did you find a good spot for winter storage? I have a great indoor place for my CS here in Elk Rapids.