Adding 2 fans to a 4-pin Molex power output connector from your PSU should NOT have any impact at all on system speed. Are you sure it was affected?
I agree with Davcon - I prefer that fans have intake filters to exclude dust, and that the overall balance provide slightly more intake or air than exhaust fans swo that the case is slightly positive pressure inside. This will ensure that at leakage points the air flows out, not in Incoming air brings dust. I admit that others disagree on that balance argument, but I like my way.