Does fresh mackerel have more omega-3 fatty acids than smoked mackerel?
Theory is a good thing, but data is always better. Especially when somebody else does the whole work of gathering and evaluating it. Luckily, there is somebody who does it for food. Following data comes from the USDA. It is very verbose, so I had to cut off most of the screenshots. I left all the lipids in the first one just to show how much they measured, and only used the data for Omega 3 in the other ones. 

The first data set is raw Atlantic mackarel. I picked Atlantic just because it was first in the list, they have several kinds. 



Sadly, they didn't have data for smoked mackerel. But as Frankie points out, you can do a hot smoking process and a cold smoking process. I think that the cooking in both is very well approximated by cooking on dry heat, resp. salting. Of course, it is possible that the smoke itself destroys more fatty acids than just applying heat or brine, but these numbers give us an upper limit for the amount of omega 3 left after smoking. 





Now we can start making conclusions. 


  First conclusion: there is something fishy about the data.


Zero standard deviation for all the values in the raw fish? Zero data points for the salted fish?! I can only assume that they just wrote a zero where the actual information is missing from the record. Still, I think we can trust the data (because the USDA has no interest to lie and because we don't have a better data set). 

Before we start making further conclusions, we should remember that these are values per 100 gram of end product. 100 g of salted mackerel isn't made with 100 g of raw mackerel! Luckily, the source also gives the water percentage of the samples (not shown on the screenshots), which is 43% for salted mackerel, 53% for cooked mackerel and 63% for raw mackerel. So, we should in fact compare the numbers per 100 g of dry matter (we assume that the cooking process neither adds nor subtracts dry matter - not exactly true for salting, but we can assume that the difference is small). The numbers are: 




  Second conclusion: Heat (so presumably also hot smoking) destroys around 40% of the fatty acids in mackerel 


This is straightforward, comes from the numbers in the table. 


  Third conclusion: The salted mackerel didn't come from the Atlantic 


Unless I have made a big mistake in my reasoning about the comparison based on dry matter, a salted fish has more omega 3 than a raw fish of the same size. The difference in data is small enough to have been caused by the choice of a different kind of fish (note that the standard deviation within a sample of the same kind of fish is 10 to 15%). 


  Fourth conclusion: Cold smoking probably doesn't destroy a significant amount of omega 3 acids. 


While the data comparison here has some problems (the assumed different kinds of fish, the fact that salting isn't the same as smoking), I think we can see the trend here. If the salted fish had lost too much of its omega 3 in the salting process, then it wouldn't have such high omega 3 values after the salting. We can assume that a cold smoked fish is also salted (my personal experience and Frankie's answer support that), so any possible preserving effect of salt should be present in cold smoking too. There is a risk that the smoke itself could destroy the fatty acids, but I doubt it. After all, the smoke doesn't penetrate the tissues very deep, so there shouldn't be much contact. 

Of course, I am not 100% sure about the conclusions above, but I think it is reasonable to assume that they are true. I have tried to make clear any possible problems. So the short answer is: fresh mackerel and cold smoked mackerel have about the same amount of omega 3 fatty acids, but hot smoked mackerel has much less omega 3 than the original.