Well, it seems your only doubt is about naval models. Usually they don't have a base at all, bar the submarines and s few others (the aforementioned Metzger). If you want bases under all your models, I think clear ones will look just fine, while sculpting waves on every ship's base would prove to be more consistent.
This said, I've left all my ship un-based, mainly for gaming purposes.
In this regard, if you plan to play with your models, you should be aware that rules-wise if a model comes with a base measurements are made from the base, if the models comes without a base (usually ships) measurements are made from the model itself (and in different ways depending on what you're measuring for. For example, iirc, turret fire is measured from the turret itself, generators effects are measured from center of the ship, broadsides in a further different way, and so on...). So while you can indeed mount ships on bases, you should then remember which model should have measurements made from the base and which ones don't.