They cost a few bucks (don't forget to factor in the cost of a case), they add a few grams to your frame, and they make tandems a bit more stiff (which ain't a bad thing), but that's about it as far as their impact.
Properly packed, S&S coupled bikes and tandems will come through travel no worse for wear than any other properly packed full-size bike or UPS shipment. As for airport hassles, very few folks who travel with their tandems -- and there are a lot of couples who do -- have encountered any trouble or undue attention when checking in their bike cases on domestic or international trips.
Our last trip was to California via ATL to SFI and then San Diego back to ATL without so much as a raised eyebrow. Just about everyone we ride with now owns a tandem fitted with S&S couplings and several have travelled to Europe every year for the past four or five years to take summer tours. No problems for them, but others who have taken full-size bikes via aircraft or who have shipped them ahead have almost all had problems; damaged cases, mis-routed cases, and the like. This was probably more a string of bad luck, but it's interesting to note that the take-a-part bikes do travel with a lot less drama.
More info on our travel tandem is here:
http://home.att.net/~mark.livingood/Ericksonpack.html