Is a crew in a docked attack shuttle in play? For example, can I use Intelligence agent when he is in the shuttle (but docked)?

No.

The attack shuttle is out of play for all purposes when docked, with the sole exception of the Phantom title.

Thanks

None of the Attack Shuttle's upgrades are in play until it is deployed, with the one exception of the title.

Docked ships basically dont exist. Not a single bit of their stats or upgrades are in play EXCEPT the title because it specifically states otherwise.

if even the crew was enabled but not the rest, you'd probably see a lot more budget phantoms docked to a ghost for the rear shot + double turret shot + extra crew slot lol.