As long as each folder uses a unique cart instance, that _should_ work ok, but it would really be better to use sub domains instead, as that would remove any possibility for session cross over. sessions are unique to the domain, so using subfolders there would be a possibility for using the same session name in the different stores.
using a subdomain would prevent this possibility since the sessions would be unique for each subdomain. even if you used the same session name in 2 of the stores, it would not be visible cross the subdomains.