No worries d@rk51d3.
Well, I think we've established that it's not happening to everyone. I can also assure you it's not an 'easter egg', although it would be a cool one. Wish we'd thought of that. It'd be very cool to see the explosion effects of all ships after some time in the museum.
What I can assure you is that it is unlikely to affect your campaign. Strange & funky things can & do happen in the museum as it has completely separate settings to the fully loaded game.
Carry on, sink em all.