Yep the disorientation comes from our sense of linear acceleration and pitch being from the same organ - as with all balance organs the ambiguity is resolved by vision (which is why when teaching instrument flying we keep harping on about trusting the instruments!) In conditions of low visual reference (night, rain, fog etc.) the strong linear acceleration of the catapult stroke can be perceived by the pilot as a pitch-up, the instinctive correction of which would be rather disadvantageous!
In the Bug the FLCS does the work based on T/O TRIM which is set for the stores and fuel load, to fly a pre-determined pitch up to shallow climb off the catapult, then the pilot takes over (and apparently they call that handle the towel rail, sources needed haha!)
For the Tomcat, the pilot follows the stick with his hand but again the take-off trim setting does the initial work, photos of the tomcat with large nose-up deflections of the stabilators during the initial part of the cat shot are apparently due to the bob-weight on the stick being pulled aft by inertia during the acceleration, which pulls the stick back.
Oh and carrier ops in DCS, excellent - the Cat is a beast to wrestle around the boat, I don't have the Bug but my clanmates comment that the FLCS makes it a little easier, but still very challenging!