"Camouflage", a novelette by Henry Kuttner and C. L. Moore, first published (as by "Lewis Padgett") in Astounding Science Fiction, September 1945, available at the Internet Archive. You may have read it in one of these compilations.
"He mentioned his decreasing use of "symbols"—for example, activating a certain control used to feel, to him, like pressing his foot on an accelerator pedal, but the feeling changed as he got used to the new control."
“"Delusions of alteration—but no delusion, my love. You see, Van, when I first turned into a Transplant, I had no standard of comparison except the arbitrary one I already knew. That was suited to a human body—only. When, later, I felt an impulse from a digger-gadget, I'd automatically feel as if I had my foot on a car-accelerator. Now those old symbols are fading. I . . . feel . . . more directly now, without translating the impulses into the old-time images."
"He said the friend would forget their friendship before the MC did."
"I've lost nothing human," Quentin insisted. "The emotional basics haven't changed. It . . . isn't really pleasant to have you come in and look at me with plain horror, but I can understand the reason. We've keen friends for a long time, Van. You may forget that before I do."
The ship, crewed only by the brain in a box, is transporting an atomic power plant to Callisto when it is hijacked:
The amplifier said. "What is this, piracy?"
Brown said casually, "Call it that. And relax. You won't be harmed. We may even send you back to Earth, when we can figure out a safe way to do it."
Cunningham was investigating lucite mesh, taking care to touch nothing. Quentin said, "This cargo isn't worth highjacking. It isn't radium I'm carrying, you know."
"I need a power plant," Brown remarked curtly.
"At one point he made a comment about watching them from "up here", and one of the characters suspected he was referring to his actual self (the brain), rather than the security cameras, being high in the ship."
"You give up," Quentin said. "I can see everything you do. The ship's a mass of traps anyway. From up here all I have to do is watch until you get close to one. I'm planning my game ahead, every gambit worked out to checkmate for one of you. You haven't got a chance. You haven't got a chance. You haven't got a chance."
From up here, Talman thought. Up where? He Remembered little Cotton's remark that geometry could be used to locate the Transplant. Sure. Geometry and psychology. Halve the ship, quarter it, keep bisecting the remainders—
Not necessary. Up was the keyword. Talman seized upon it with an eagerness that didn't show on his face. Up, presumably, reduced by half the area they'd have to search. The lower parts of the ship could be ruled out. Now he'd have to halve the upper section, using the celestial globe, say as the dividing line.
"The ship was powered by a (fusion?) reactor that could run on a wide range of matter. The fuel was poured through a one-inch grid in the ship's floor."
There was only one requirement for fuel; it was best to filter it through a wire screen with, approximately, a one-inch gauge. And that was an arbitrary matter, for convenience in setting up a standard of fuels. For the rest, atomic power ate anything.
The brainship "eats" one of the pirates:
"I think you'd better give up," Quentin said.
Brown was floating across to join Fern. "Never," he said, and simultaneously four G's hit the ship with the impact of a pile driver. It wasn't forward acceleration. It was in another, foreplanned direction. Fern saved himself at the cost of an almost dislocated wrist—but the looped line rescued him from a fatal dive into uninsulated wiring.
Talman was slammed down on the balcony. He could see the others plummet to hard impacts on unyielding surfaces. Brown wasn't stopped by the floor plate, though.
He had been hovering over the fuel-feed hole when the acceleration was slammed on.
Talman saw the bulky body pop out of sight down the opening. There was an indescribable sound.
Quentin lets his old friend get away:
"The door's open," Quentin said.
"You're letting me go?"
"I told you in Quebec that you'd forget our friendship before 1 did. Better step it up, Van, while there's still time. Denver's probably sent out helicopters already."
