Yes, absolutely. I believe Ferrari's official stance is that the car was certified for "a moment in time," essentially. The certification may still valid for another year or two, but there are no guarantees that the car would conform again once it leaves Ferrari.
A good faith move by Ferrari would be to certify cars with some aftermarket accessories such as exhaust or wheels and documenting those particular and reversible details when the originals are presented without nickel and diming the client to change them out. If the car is sold, the buyer can see what should be there in the nice red covered book.
I agree, I got the Classiche on my 355 before the heavy discounts, but the exhaust swaps were 25% of my costs and 75% of my headache.
I'm surprised Ferrari doesn't claim ownership of the Red Books and force forfeiture when certification renewals aren't completed in a timely manner. Whoops, I shouldn't give them any ideas.