I think that unless the remains are in a closed compartment where the batteries were located they are likely to be unaffected. It seems likely that bulkhead hatches would have been secured prior to the sinking, but implosions, leaking valves, and other damage might have opened those compartments to the sea.
The real problem is probably not the gases, but the acid contained in the lead-acid batteries. Under some conditions this acid is likely to leak from the batteries and if confined, would affect the compartment. However, if there is enough water to dilute the acid, it is likely to have very little effect more than a few feet from the batteries.
Seawater has a pH of about 7.5-8.5, so it is slightly alkaline, and contains many salts that act as buffering agents, so where there is any circulation of seawater at all, the acid is unlikely to have had much effect on anything.
You don't mention the time period that the sub has been down, so it is hard to speculate on what condition remains would be in. Marine organisms are likely to have taken a toll. The relatively recognizable surfaces visible on the wreck of the Titanic are probably only that clean because of the extreme depth and near-zero bottom temperature.
Here is an interesting article on submarines as a class of archaeological site that discusses some of the political implications:
If you are looking at a U-boat you should visit u-boat.net:
Something to consider about U-boats is that they used liquid mercury as ballast. This might be a hazard, or might even have some salvage value. Many years ago I was offered a job working as a commercial diver in the salvage of a U-boat in Central America. I passed on the opportunity because the pay was sketchy, but have often wondered if I should have taken the chance.
Another site with information on submarine technology:
The other thing you must consider is the depth. At very deep depths in the ocean there is a level known as the Carbonate Compensation Depth (CCD). This is often at 4000 to 5000 m, so it is probably unlikely to be a concern. Below this depth anything with calcium in it will eventually dissolve, which includes human bone. However, there have been remains recovered from shallow (30 m) water from ships that went down in the late 1700's. The HMS Pandora is an example.