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1. How should I document the interface?

See http://ros.org/wiki/move_base for the current 'best practice'. It's not great, but all that's possible now w/o someone writing a plugin for rosdoc to handle actions the same way we do with msg/srvs.

1. Is it considered "best practice" to check in the generated msgs from the .action files?

You should never check in generated files.

If you wanted to get very clever, you could run rosdoc on your package against a built tree and save the msg docs and link to those, but that's still not an ideal solution to #1.