How can I use pathauto to generate URLs for deeply nested vocabularies?
Try something like this as your vocabulary pattern:

[term:parent:parent:parent:name]/[term:parent:parent:name]/[term:parent:name]/[term:name]


And your last question should go away.

Just be sure to repeat the parent: part at least as many times as max term depth expected in your vocabulary. Pathauto will smartly skip overhead items.

I know it's not super-scalable, but it works for me.