If you are using cs-cart ULTIMATE (not MultiVendor) then:
1) SSL's are by domain so if you have example.com and example.com/store2 then you only need 1 SSL However, if your customers will access your storefront as store2.example.com then you would either need a wildcard SSL certificate for *.example.com or you would need separate SSL's for the main domain and the sub-domain.
2) Themes are independent so yes, you can use different themes in different storefronts
If you use Responsive them then there is no need for separate stores to present to different devices unless you absolutely have to have a mobile-only site.