Yes, he has to empty his room.
Yes, there is storage - the "baggage locker" - make sure you tell him to lock his stuff in a foot locker or similar.
When he returns, he will be a third classman, all be it, a "super plebe" the jargon for a third classman who hasn't been to sea yet - sorry A splitters, I'm a B split bigot and have been since 1979, old habits die hard. In any case, yes, he'll be able to have "everything" he had in his room before there now. He as part of the Indoc Detail will be expected to maintain the high military bearing they reflect during Indoc, ahem, snicker, snicker <also a career Zombo here>.
He will likely have some fun during Indoc and he will have checked a box early in his KP career that he'll want to have checked if he ever wants "big boards" etc.
It's not all bad for him, you can engage the autopilot on the helo and take it up to a higher altitude though I'm sure from the tone of your post you, your spouse and your son were all hoping for a nice, enjoyable summer break to celebrate making it through that first year - don't blame you congrats and continued good luck to you and yours.