First, should references between aggregates always be done through ID values and not actual object references?
Not really - though some would make that change for performance reasons.
For example if I want details on the customer of an Order I would need to take the CustomerId and pass it to a ICustomerRepository to get a Customer rather then setting up the Order object to return a Customer directly correct?
Generally, you'd model 1 side of the relationship (eg., Customer.Orders or Order.Customer) for traversal. The other can be fetched from the appropriate Repository (eg., CustomerRepository.GetCustomerFor(Order) or OrderRepository.GetOrdersFor(Customer)).
Wouldn't that mean that the OrderRepository would have to know something about how to create a Customer? Wouldn't that be beyond what OrderRepository should be responsible for...
The OrderRepository would know how to use an ICustomerRepository.FindById(int). You can inject the ICustomerRepository. Some may be uncomfortable with that, and choose to put it into a service layer - but I think that's overkill. There's no particular reason repositories can't know about and use each other.
I'm confused because returning a Customer directly seems like it would make writing code against the model easier, and is not much harder to setup if I am using an ORM like NHibernate. Yet I'm fairly certain this would be violating the boundaries between aggregate roots/repositories.
Aggregate roots are allowed to hold references to other aggregate roots. In fact, anything is allowed to hold a reference to an aggregate root. An aggregate root cannot hold a reference to a non-aggregate root entity that doesn't belong to it, though.
Eg., Customer cannot hold a reference to OrderLines - since OrderLines properly belongs as an entity on the Order aggregate root.
Second, where and how should a cascade on delete relationship be enforced for two aggregate roots?
If (and I stress if, because it's a peculiar requirement) that's actually a use case, it's an indication that Customer should be your sole aggregate root. In most real-world systems, however, we wouldn't actually delete a Customer that has associated Orders - we may deactivate them, move their Orders to a merged Customer, etc. - but not out and out delete the Orders.
That being said, while I don't think it's pure-DDD, most folks will allow some leniency in following a unit of work pattern where you delete the Orders and then the Customer (which would fail if Orders still existed). You could even have the CustomerRepository do the work, if you like (though I'd prefer to make it more explicit myself). It's also acceptable to allow the orphaned Orders to be cleaned up later (or not). The use case makes all the difference here.
Should I instead have a CustomerManagment service which handles deleting Customers and their associated Orders which would references both a IOrderRepository and ICustomerRepository? In that case how can I be sure that people know to use the Service and not the repository to delete Customers. Is that just down to educating them on how to use the model correctly?
I probably wouldn't go a service route for something so intimately tied to the repository. As for how to make sure a service is used...you just don't put a public Delete on the CustomerRepository. Or, you throw an error if deleting a Customer would leave orphaned Orders.