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I use SpeedHacks because my system's not good enough (2.8ghz C2D CPU).
Since I have speedhacks game runs 60fps, but GS is around 90%.

The problem is I feel I got input lag, whether it is keyboard or gamepad - even though I get 60fps - am I having this problem because I'm using SpeedHacks?

I can feel the input lag here a lot because because I got the same game on NullDC-NAOMI and there is zero input lag there

Yes, the VU cycle stealing hack when it is set in too high will cause wrong FPS reading, so in fact you are not getting full speed. Try turning it down