Nah...I can go to a space dock and swap out the weapons, equipment and such fine there, just won't let me do it on the fly, well one weapon slot will.
For example the ship I have has a fwd phaser, fwd torp and rear phaser.
I got a Quantum torp for kicking some alien's behind, which of course I would replace the fwd torp with...however when you dbl clicked on it, it would only slot itself into the #1 position where the fwd phaser was....however if I went into space dock, I could delete the reg torp and replace it with the quantum one.
Same with the rest of the equipment.