3-way SLI GTX 980:
Advantages:
1) High frame rates compared to 2-way.
2) More higher resolution support. (also, you can get smooth play on three 1440p monitors)
3) More future proof.
Disadvantages:
1) Poor scaling when going to higher resolution.
2) More noise due to more fans in total.
3) More heat due to insufficient gap between three cards, between the three cards and the case. (i.e. needs a full tower case for better cooling).
4) Complete waste of money if three GTX 980s are hooked to play in one 1440p or 1600p monitor. (Even two GTX 980 is enough for single 4k monitor gaming). Also, there will be more powerful and efficient GPUs in near future for lesser money (due to competition) which you can't buy since you've already accumulated with three 980s.
Note: Nobody can notice above 60fps all the time.
2-way SLI GTX 980:
Advantages:
1) Less heat and more power efficient.
2) Less investment .
3) Very less scaling issues.
Disadvantages:
1) Comparatively lesser frame rates than 3-way.
2) Can't get enough frame rates in 4K or three 1440p monitors.
Hey, if you have lot of money to spend, will never want to upgrade your system for several years, will game now in one 1440p monitor and then upgrade to two or three 1440p monitor in near future, just get 3-way SLI.
If you are earning more money (i.e. you can upgrade your system any time by investing money), just stay with 2-way or even one GTX 980. Simply don't waste money.
Even a single GTX 970 is enough for single 1440p monitor to play all games at ultra.