I'm using iPhone 6s plus 64Gb with 9.3.3. Does jailbreaking have an effect on performance/speed?
No. Jailbreaking itself doesn't cause slowness. It's what you do with that that causes trouble. And since you have a 6s.. I wouldn't bother jailbreaking it until iOS 10, since it's so close.
I guess I would ask what features or functions are you hoping to gain. Back in the"early" days there were lots of reasons to jailbreak (besides just plain fun): 3rd party apps, springboard, customization, tethering, and other hacks. For me, iOS has acquired all the features that I got from jailbreaking, without the extra hassle.
Unlike rooting android, which users perform to enhance performance by overclocking, upgrading to a better kernel, and customisation, iPhone is pretty well optimised in this aspect, so one of the obvious reasons someone would find a need to jailbreak it would be just the customisation. To clear your doubts, this will not slow down your device but could sometimes make it unstable when some unsupported tweaks are installed. Rest assured jailbreaking is fun. But for an iPhone 6s which is already very fast and optimised, there is hardly any need for jailbreaking. Though the final call is yours.