Indeed, I'm not sure in what situations this tradeoff of cons/decons- for lookup-speed is helpful. If I just need fast lookup, I'll use a mapping structure (hashtable, balanced binary tree, patricia trie, etc). If I need reasonable lookup speed and also standard sequence manipulations, finger trees or ropes seem like a better choice. They're more complex, but if performance is an issue, then it's probably worth it.
Also, a bug/design flaw: You can't store NILs in the terminal position:
> (trellis 1 2)
(1 (2))
> (trellis 1 2 nil)
(1 (2))