Aeon destroyers were the best destroyers, at least until the last path, but that does not mean that they were overpowered. Aeon has largely the worst t1 navy. And almost no navy fighting or bombing capacity on croisers. They dont have much else on t1-t2 level. For someone who dont know how do play (or rather knows less than enemy), and gets crushed by Aeon navy, it might seem, that he lost because of destroyers. While in reality navy is much more than only building destroyers.
In perfect micro conditions you can dodge all Aeon destro surface shots. And in real game it is not rare that they miss around 50%. While Sera destros are supposed to hit 100%. So haveing beam weapons on Sera destros is a big advantage on navy, and true, as you said, can be disadvantage on navy-to-land in some conditions. But note also, that Sera croisers can hit far inland, kill plane waves and force navy to move/micro.
Personnally, when fighting someone at my level or stronger, I would prefer beam weapons (that dont miss), because winning navy is usually harder and more important than hitting beaches in most effective way.