Back to the original question KSP is unoptimized, that's what there's been a digression on. Mods absolutely can hurt performance. I've seen as much as an 80 - yes, eight zero - percent fps drop from a buggy mod. Your system is virtually identical to mine - I have a Phenom II X3 overclocked to 3.1 GHz, a GTX 750 Ti, 4 GB of RAM, and run Xubuntu 14.04. This means we can make a comparison. On a bone stock install, but with my normal game settings, I've been able to get the start of lag at around 100 parts. But that's just the real edge of it - the MET clock flickers yellow, with the game running at 0.9-1.0x normal speed and maintaining close to 25 fps. And it does depend on the parts, some affect performance worse than others. (For example, I flew the big stock plane and with the cargo bays open it was measurably worse than with them closed.) If you're noticing that kind of slight framerate drop and finding it objectionable then KSP might not be the game for you. If you're getting what I'd call serious issues, let's say below 15-20 fps, the MET clock solidly yellow or even red, something that a total non-gamer would notice, then I'd look at whether one of your mods is responsible.