I think it depends on whether the coin in question was only available as part of a mint set, or if it was a circulating coin.
Take, for example, the snowy owl dollar -- the only way to get it is to buy the mint set. You're a dollar collector. So, do you break open the set for the dollar, or do you leave it as is?
It all depends on what you'd do with the coin once you got it out. Do you put your coins into 2x2's, or into some sort of folder? If you do, then you will have noticable spaces where they are supposed to go, and you will want to add them.
But then, you wonder if you aren't actually losing money by breaking the set open, and therein lies the dilemma. Yes, you could recoup some of this money if you sell the other coins, but you have to find a buyer for them first. Conceivably, there may be a fifty-cent piece collector out there who would be glad to get the one you want to sell, and you may be able to get rid of the other coins the same way, but I think the likelihood of this would drop as you go down in the denominations, unless of course, there are short strikes in them, or some other reason people would want them.
Of course, then, your collection looks better because it's complete, and that might make you happy enough to ignore any shortfall you incur. If you're satisfied with that, fine.
Naturally, the easiest way around this is to buy the coin you want from someone else that has broken the set for a different coin they wanted. But, of course, this doesn't happen as often as one would like, and you might wait forever for the coin you want out of that year's set (although this has been shortened by being able to shop on the internet).
Personally, I don't break them. I do collect loonies and in the cases where there is a "mint set only" coin, what I do is scan a 2x2 on Paint, and put the image of the coin in question in the "hole". On the white part of the 2x2 scan where one would normally write, I do the usual write-up, but add the wording below, "ONLY AVAILABE IN MINT SET". I then print the scan, cut it out, and glue it to the front of a 2x2 and put that in my holder. I have the coin in question, but it is in the mint set, but the coin page still looks complete because of the placeholder I have made.
I find that this does the trick, and does it in a way that satisfies me.