SMC Fan Control just allows you to set a higher minimal speed, the normal hardware/OS X system of fan adjustment is still at work.
The normal OS X/hardware system is when the CPU gets hot, the fans increase speed to keep the temperture down. It all depends upon what the CPU is doing and the ambient room temperture being able to remove the heat from the CPU's.
Increasing the fans speed a tiny bit, say a extra 1000 RPM's from 2000 RPM and leaving it that way, keeps the CPU cooler all the time, so when it does start working, it doesn't get as hot as quickly because it's working from a lower starting temperture.
If your gaming or using the CPU heavy, well it's going to get hot regardless and OSX is going to kick in and race the fans to 4000+ if it needs too. But most times people don't place great demand on the CPU's, they want to just be able to lower the temperture a bit so it's more comfortable and that's what SMCFanControl can do.
You shouldn't be having the fans on 4,000 RPM all the time, that's excessive and yes, could wear them out faster. However a fan is less expensive to replace than a logicboard. 🙂
You might want to run a Hardware Test, one of your fans might have stopped working and that results in a hot machine. You can replace the fan yourself, but if it's under warranty/AppleCare you should have them do it.
https://support.apple.com/kb/ht1509