Why does the MSI GTX 980ti only have two fans?



It depends on the size and make of the 3 fans being used. Also, noise can be a varying factor on 2-fan cards to 3-fans. If both are running at 100% speed, the 3-fan card will be louder, but if the 3-fans cool better, they can spin slower. Pretty much, a GPU company isn't going to release a card with an insufficient cooler.
 
If I was going to purchase an air-cooled GTX 980 Ti for my system, it would be an EVGA brand ... all of which have either one fan or two.

All of the manufacturers have different requirements for their graphics cards, and those that make two-fan models obviously think that two fans are enough to cool their cards.

Why ask why? Even if we could provide MSI's exact reasons for going with two fans, what good would that do you? If you don't think a two-fan GPU will be cool enough, just buy a three-fan version. There are plenty of both to choose from.