You can create them, they just won't have attack animations until we figure out the state files I mentioned. To me, the animations are far less important than the mechanics, so I'd say to go ahead and make those classes anyway. (This is why my mod still uses a lot of placeholder graphics for its units; while custom 3D graphics would be nice, and I'm still working on them, it's more important that the underlying game balance correctly. Aesthetics are a secondary concern.)
One other thing I thought of: it could be purely internal to the engine. The determination of where the units stand when the combat animation starts could easily depend on the combat classes of the two units involved; if you go into the artdefines_unitmembers file you'll notice that many units have two weapon definitions, one for normal combat and one when defending from air units, so if the "normal" one leads to some internal table lookup that keys off of combat class then there's nothing we can do about it. (This'd also explain why the air units still work.)
If this is true, then we'll have to wait for the DLL to even have a chance to change it.
Side note: In my mod I had no need for a separate submarine combat class, because both subs and destroyers upgraded to a single vessel in the future eras. So while land promotions on a sub might be useless at first, once you upgraded the unit they'd be very handy. But in a vanilla environment you don't really have that option.