Actually spiking guns and other equipment already is an automatic part of the game. Every time I've besieged a town/city into submission -- the defender surrendered -- I've never gotten a single piece of equipment from those surrenders. When Pemberton surrendered Vicksburg he surrendered 172 guns along with it. He most certainly had adequate time to spike them were he inclined. In-Game you only capture equipment during a battle, which hardly happens nearly as often as it historically did.
What is also askew In-Game is actually capturing units. As far as use, when you capture a 'unit' you realistically can only capture the equipment. You may also capture the troops, but they won't fight or work for you
. ..
So a captured battery should actually only be the guns and not an entire 'unit'/counter. Baring that in mind, guns, ships ans supply trains you capture cannot logically have the status of being a non-completed unit. You should have to crew them with your own troops, and if the unit was not completed, and/or damaged in battle, they should simply have that many fewer guns/wagons/ship's cannons as the case may be.
Were this the case, there would yet be situations where spiking guns would be a logical, strategic solution; for example if the guns were fort batteries or coastal artillery. You could hardly expect to escape a besieged town with these, so the only logical solution would be to spike them before or while trying to escape.
As far as capturing ships carrying guns, land units being transported
will fight at sea. And from my experience as long as a fleet has a means to fight it will. Fleets of transports only not carrying land units will often be captured if they cannot escape a battle.