Yes.
First design the new ship, the easiest method it copy the design of the Mk1 destroyer then make the appropriate changes. Then have one of your shipyards retooled to build the new design, then move some of the mk1 destroyers to the planet with the shipyard , then select the refit ship command for the shipyard select one of the mk1 destroyers and then select to refit it to a mk2 destroyer.
If the changes are very large it may be cheaper and faster to build new ships.
(Make sure you select the right options I managed to refit a 30,000 ton carrier into a 4000 ton survey ship by being careless)
