Q1: when federated, do you still have service in Server and can they be in folders?
Yes, once you federate, all services will still exist on the server in their original folders, they're just automatically added as items to the portal. You'll need to move them into folders yourself within your My Content if you want similar structure, but where they exist in Portal doesn't affect how they're stored in Server, (security, of course is affected, as the security store will change).
Q2: are services in Portal separate from these? Or, are the item numbers you mention actually pointing to the Server services.
Portal is always storing references or pointers to services. You can publish directly to Portal, (creating a hosted service), or you can publish to Server directly, (traditional map service). In either case, a service is still spun up on the Server for you and an associated item is created within the Portal. The item numbers, or item IDs associate the item in Portal to the service in Server to establish the link for security/sharing.
Q3: what causes the item ID duplication?
Simply the act of federation adds all services in the Server as items to the Portal, regardless if the item already exists or not. We've had some discussions on how to handle this, but nothing in place yet.
Q4: will your Server services still be there and possibly in folders, or do they all need to be recreated?
Once you unfederate, the security for services will be controlled by the Server again. I believe your original security store, (the same users, roles, etc), will be available but I haven't tested that. You may have to secure your services again, though. The services will continue to exist, you won't need to recreate any.