Can you shoot the ships off the surface of a Kraken? And if you blow up the ships that are on the surface of the Kraken, do we think it's going to damage the Kraken?

It will damage them a little. Depends what ship explodes and what's in it. It's one of those endless questions. But yes.

Fully loaded Freelancer MAX with the brim of fuel.

Yeah. It's going to do a lot of damage.