Anodizing converts the surface of aluminum to an oxide that happens to be a ceramic. Hard anodizing produces a deeper oxide layer for better resistance to abrasion. The oxide is inert, and hard, but it's also porous/ microcracked.
Reports of reduced seawater corrosion in anodized aluminum vs. bare aluminum are probably the result of the traditional penetrating dye/sealant applied after anodizing.
One time I let someone talk me into a 'clear anodized' finish on some medical equipment parts. What we got instead was anodize with no coating/dye. We didn't realize it when the parts arrived, but after a month in (indoor, conditioned) storage, the parts were corroded too badly to use. They looked like very old zinc or terne plate.
If you do decide to go with anodizing, make sure it's colored, so you can verify that the sealant has been applied, and don't expect miracles.
I personally would favor powdercoating, or polyurethane paint.
So when you say "dont expect miracles," does that mean you would avoid Al all together even with some type of coating (power, polyuretahne, etc) for long term sea water deployment (6-12 months)?
This is for an instrument housing, so if it leaks, the instrument (and electronics inside) will fail immediately.
Obviously I know there are better materials out there (Ti, Duplex) but cost is an issue.
It means I wouldn't use anodized aluminum in seawater.
Above the waterline, powdercoated aluminum looks great and retains its good looks for a long time, but in the water, I'd worry about a pinhole compromising it.
I'd go with multiple coats of polyurethane, in contrasting colors so you can see when the film has been compromised.
I'd also use sealed connectors and conformal coating on the electronics inside, just so they'd be salvageable in case of condensation or a small leak.
I beleive one of the 5000 series Al's is rated for salt water. Possibly 5052. I agree with Mike, do not use the 6061 Anodized. Powder coating has its downfalls also,, pinholes, cracks, thermal expansion etc...
The 5000 series aluminum alloys are generally considered good for marine applications, and 5054 plating is a common material for hulls. Please note, though, that the underwater hulls are still usually cathodically protected with zinc anodes.
Some underwater camera housings are made from machined 6061 AL, which is powder coated. I have one and I don't have a problem with corrosion if I use dielectric silicone grease before I screw on the stainless accessories.
Some high end speargun handles are made from cast 351 AL and hard anodized. Some of my speargun handles are over 15 years old, and I have used them frequently and I don't have a single handle with a corrosion problem. I like hard anodizing. It is much stronger and abrasion resistant than any paint or coating.