I wouldn't want to enclose smelly shoes into a container of any sort. Clearly smelly shoes need to be aired out. Most importantly, you should try to get to the bottom of why your shoes smell. Seriously. My athletic shoes don't smell. Why do yours smell?
Is it because you wear them wet and don't properly dry them when you get home? If you are running in the rain, toss your shoes into the dryer when you get home. Do you wear the same pair of shoes every day? Shoes need a break to air out between wearings. It's best to own a few pairs of shoes and alternate to give them a few days to air out between wearings. Do you have athlete's foot? Treat that problem so your shoes don't smell.
Are you wearing socks made of material that make your feet sweat and don't wick moisture away from your feet? Any synthetic material in socks is the worst for this. Get socks made of natural materials----not synethetic blends---100% cotton, 100% bamboo, 100% wool. A blend of NATURAL materials is good too.
But wool athletic socks are the best for wicking moisture away from feet. Wool dries quickly. There ARE wool athletic socks made of thin matieral. Expensive but well worth it. Look here:
wool athletic socks - Google Product Search
Are your shoes made of natural materials? Synthetic shoes make feet sweat and smell. Stick with athletic shoes that are made of real leather or a canvase material made of a natural fiber.
Seriously consider tackling the CAUSE of your smelly shoes instead of a place to hide them. Enclosing smelly shoes will only cause mildew and/or yeast to grow in your shoes. Shoes need to breath!