Only answering the ones I know.
- Will it prevent passage or slow the units down as they cross the water?
Yes. You will eventually have to go around water, or over it (bridges), not sure what else. Also, naval things are planned. I'm ONABOAT!
- If so will this apply for all units or are there exeptions to this rule?
Pretty sure it will impact all units.
- Will ships/boats be implemented at some point to further trade - specifically quantity?
Yeah, they said navy stuff and boats, docks, new buildings related to waterways, etc will be added. They have lots on the drawing board and are still organizing what to add (I think).
- Will cities lying adjacent to water be more vulnerable to attack?
That depends. Enemies will have to cross the water to attack you from the side with water. Otherwise their attacks will have to come around the water.
- Lastly - Will there be monsters below?
Sea monsters? possible. Heard it discussed but I'm no authority on the subject. I think the staff themselves are kicking a lot of ideas around to make it as cool as possible when they eventually code it all