A lot depends on the brand of canned tuna you are buying, since that determines the canning process.
Tuna are initially frozen (especially if the vessel is far out at sea), then gutted and pre-cooked for 45 minutes to three hours. The fish are then cleaned and filleted, packaged into cans, and sealed. The second cooking of the tuna meat (called retort cooking) is carried out in the cans, for a duration of 2 to 4 hours.
So, judging by this process, the long cooking time could be what depletes nutrients, since the tuna is cooked at high heat about 212 degrees Fahrenheit for hours.
Nutrients that tend to be particularly sensitive to high-heat cooking are usually water-soluble, with Vitamin C (75 % depleted), Thiamin (75%), Folate (75%), Potassium (70%); to a lesser extent, B-vitamins (around 50-60% range depleted), Niacin and Riboflabin (40-50%); selenium in animal form seems to be a lot more stable and is hardly depleted by cooking. Most data out there is for the effect of heat on vegetables, which contain more water and are more susceptible to damage via hight heat cooking.
I have not found anything specifically on tuna, but here is a document on nutrient retention after cooking which has tested a type of fish (finfish) http://www.nal.usda.gov/fnic/foodcomp/Data/retn5/retn5_tbl.pdf
However, as I said, this depends on how nutritionally-conscious the company making the product is. Very long exposure to high heat (in order to kill any potentially harmful bacteria), as I suspect is the case in a lot of the commercial tuna probably depletes nutrients a lot more than in the studies above. Also, the fact that fish is usually cooked in cans could make leeching of harmful substances from the can surface a problem, too (especially varnishes used to polish the metal); this is especially the case with BPA.
Undoubtedly, fresh, wild-caught tuna cooked rare will be more nutritious than canned, but the occasional BPA-free canned tuna isn't going to harm you, especially as the fish used for canning is usually smaller and smaller fish tend to accumulate less heavy metals like mercury.
Don't worry too much about it,
Lots of Paleo love!