You don't deal with Barbarians in Civ, Spores in Alpha Centauri, Antarains in MOO2 or Minor Races in GalCiv every 12 minutes. Plus, those elements are more flavor or difficulty enhancers than vital cogs to the game's engines. Would Civ be any different if there were no barbarians? Not really. The same thing can be said about Spores and Minor Races (which can be turned off). Plus, those elements fade in importance as the game goes on. Pirates get weaker and easier to deal with as the game goes on, but you still are dealing with them every 12 minutes.
Pirates are apparently an integral part of the game in Sins. Beyond the silliness of the "pirate" nomenclature (if the Antarians in MOO2 had been called Killer Klowns, what kind of reaction do you think that would have caused? I don't understand why there isn't the same reaction to "Pirates" in Sins, especially in the wake of the redefinition of Pirates in popular culture caused by a certain series of Disney movies), the problem is that, depending on who you believe, the Pirates are being used as a crutch for either the AI, economy focused players or as a check against inflation and on the game's economy as a whole. That's pretty disturbing, isn't it? That space pirates are so vital to Sins' AI or economy functioning? I don't know. It really bothers me, perhaps more than just the annoyance of actually dealing with the Pirates.
Wow, just wow. I wonder what difficulties that you have played on. Just on Noble alone in Civ 4, I see a steady stream of Barbarians. Spores became strong in Alpha Centari, I mean a lot stronger. Antarians were constantly around being a threat and if you were the lead player you got smashed a lot. Dread Lords are not turn offable, unless you turn off Random Events.
As far as the Pirates go, I just straight ignore them. If they attack me, I stop the attack and move on. I always have a defensive fleet around my main core of planets. Once you defeat the Pirate Base, there are no more pirates in your sector.
I don't really consider them a crutch or a threat at all, unless I'm completely unprepared, then that my fault. They are just a neutral party that attacks other players, and unlike the Barbarians, Spores, etc, you can influence their decisions.