The shuttle Sakharov was apparently returned to the ship's shuttle bay where it continued to perform service until at least 2369. It was seen again in Chain of Command, Part II where it was used by Riker to plant mines on the hulls of Cardassian ships.
The Calamarain survived the encounter with Q unscathed. The script refers to them simply being "blown away". The other Q (Q2) expresses no upset at his methods, indicating his approval for what Q has done; presumably transporting them back to wherever they normally live and returning them to their normal size.
He blows on the palm of his hand. The glow is blown away. Q2 reacts,
They make a return in the novel EU Q-Space, where Q expresses no surprise that they're hale and hearty
“Captain!” Data said emphatically. “Tachyon levels are multiplying at a vastly accelerated rate.” He turned to face Picard. “It is the Calamarain, sir, and they are approaching rapidly.”
“Oh, them again,” Q said without much enthusiasm. He had not been nearly so blasé, Picard recalled, when he faced the wrath of the Calamarain without his godlike powers. “Hail, hail, the gang’s all here.”