Most likely not. I wasn't able to find my weapons, and woke up in an entirely different outfit. If they strip you of all possessions or things you are with as you arrive, Akamaru may be one of those. Not to mention, if you two arrived together, why not Akamaru? That's the part that doesn't make sense the most. He should be with you guys anyways. No one has reported Akamaru, and Shikamaru hasn't stated anything about him that indicates he's here.

Not to mention, the thought of him roaming the country side wouldn't make sense considering how well developed his senses and speed. If he was lost, he'd have ways of signaling, right? And isn't Team Kurenai a tracking team anyways?

[ She doesn't waste any time stating all of this, and, her methodical and direct way of stating this has the tact of an angry wrecking ball on every drug ever. ]