The Zodiac Pro as you suggest has two bungs in the hull. The small thumbscrew version on the hull. This is for the hull void below deck (which rarely fills up), and in the water this is below the waterline. You're only likely to get a trickle of water from the anchor locker or from screw holes in the deck if it's not sealed properly with sikaflex. This bung can only be opened upon retrieving the boat to shore.
The second bung on the transom is in the drain-well. This is again below the waterline. It's got a plunger type mechanism and is only removed when the boat is retrieved, or the boat is underway to remove water, then re-seal.
I used to have a Zodiac Pro 7-man (smaller version of 9-man) which is basically the Pro 500. On the west coast of Scotland I'd leave it at a local pier for my annual 2-week holiday. If there was a heavy downpour, then it could flood the deck with 2-3 inches of water easily. It didn't cause any major issues, as long as you don't have things lying about on deck. The battery is likely to be at the transom in a battery tray. Not a great location. Better suited shifting it to the console. There should be a tray in the console where it could be housed. That leaves space for a fuel tank underneath or under the bench seat. Some Zodiac 500s came with an integrated fuel tank under the deck, so problem solved.
If you go for an auto-bilge there's a danger you could run the battery down. Most Pro 500s will have a 50 or 60hp engine, so linked to a single battery. If you do opt to go for one, look at possibility of battery trickle charger from a portable solar panel.
Not sure how practical it is to fit a cover on the boat while its at berth. I suppose it's all about access. Even if the boat fills with water, you'd have to leave it for weeks to see it fill up. A trip one or twice a week to bale it would be required.
I'd also run the hose over the transom if you opt for auto bilge pump. More details here: Bilge pumps in small RIBS
If the boat is in the water for extended period of time you have two choices to avoid marine growth. Paint on a copper-based anti foul paint (your hull will never be the same again) and can effect resale value, or retrieve say one a month to jet-wash and scrub.
Good luck anyway!