Cobras do have low freeboard at the stern and the batteries are low in the engine compartment bilge. Moving them up, possibly to the sides of the engine compartment would be a good idea.
I can't remember where the engine air intakes are, but it might be worth blocking them off and fitting some to the top of the engine box - as per Pacifics.
Running large bore pipes from the deck, through the engine compartment and out through the transom might help with drainage - but the outlets will be a long way below the water - you'll need long trunks and remote operation for them to be useful.
Most boats have inadequate bilge pumps fitted, especially in an engine compartment. A 500gph is easy and cheap for a boatbuilder to fit. 2000gph, or more, with a reliable float switch is really what should be fitted.
Regarding other comments about coding and transom height. The code does not specify a transom height - it asks for freeboard of 250mm. A Pacific fulfils this even though the "transom" is a small lip. Whats important is sole height to give you the freeboard.
An Arctic 20 has the same type of outboard brackets as an Atlantic and no "transom" as such - but passes because the deck is 250mm above the waterline.
I'm glad no-one was hurt and it sounds ike the boat will be OK.
One final general point - probably for others more than you.
Regarding contacting your insurance company at the earliest opportunity that is good advice. However, if the incident was on a Saturday, waiting to call your insurers on Monday might be too late to carry out effective first aid.
You should act as if you are uninsured and arrange to have first aid work carried out as soon as you can - within 24 hours if at all possible. If you leave it a few days you could be looking at a complete engine rebuild. If you get it started within a few hours of the event you might just be looking at a new starter, alternator and parts of the loom.
Better luck next time!