Yeah, the armor is heavy. They (astartes) are heavy. They would sink!
I would like to see some naval/aerial combat, but not at launch. I still want them to be important however, because oceans are big, and 40k is all about being big.

I had a thread on how they oceans can be used gameplay wise without vehicles such as boats (at least, player controlled)

http://forum.eternalcrusade.com/threads/bodies-of-water-oceans-beach-assaults-strongholds.283/

Some glorious beach assaults, just what EC needs

Underwater combat would be a cool feature, especially if ranged weapons were restricted beneath the waves. I'm fairly sure all the factions will have done battle across all types of terrain in their millennia-spanning careers.

I'm left only with an image of a terrified space marine wearing armbands refusing to jump into the water to play splash-fight with a CSM.

It would be a cool to see, but I won't hold my breath...