I had the same problem(s), subscriptions created with uid = 0, and also role not assigned because the user was considered anonymous. I fixed the role problem cloning the 'Update order status on completed checkout' workflow configuration, and removing the condition 'check if an order can be shipped' (I use Ubercart 1.3, upgraded from 1.0)

That doesn't fix subscriptions with uid = 0, so I wrote with this query

update uc_subscriptions set uid = (
select uid
from uc_orders join uc_order_products using (order_id)
where uc_order_products.order_product_id = uc_subscriptions.order_product_id)

which is a dirty but working solution as each subscription is tied to an order which actually has the proper user id.