Grossly over-simplifying: A v8 crankshaft is (obviously) not straight. The big counterweights it has are there to balance out the mass of the big end of the connecting rods (as you mentioned) and ALSO to cancel out imbalances caused by the fact that the crank has to "push" or "pull" on the piston to get it to reverse its motion twice every turn of the crank. In a straight-six, flat four, and some other engine layouts, all those particular forces are cancelled out by another piston that is moving the equal-and-opposite way, and you just have a second-order effect because the pistons are at different places along the length of the crank. But in a typical v8 (we'll leave out the fact that there do exist "flat crank" v8s, but none are found in common production cars) the piston motion forces are NOT cancelled by other pistons, they're cancelled by deliberate addition of counterweights to the crank, and they have to be fine-tuned to match the actual weight of the pistons. So if you now remove some of those pistons or even replace them all with a lighter or heavier weight piston type, the crank will be out of balance.
"Mechanical imbalance" just means that the shaft is out of balance. Like a washing machine with a quilt wadded up on one side in the spin cycle.