Either way, it doesn't matter. Create a links table and load that after loading all the nodes in their various types. That's the cleanest solution. Loading the links at the same time as the nodes is going to run into problems with cycles. But, you already knew that.

An alternate solution is what Data::Dumper does and that's to keep track of what nodes have been seen before and stop following the tree when you find somewhere you've been. I don't know if that will work, given the code you've already written.