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We saw that there is a signify variation in S-Parameter results of signal nets from including/excluding the power nets VDD during simulation in Power SI tool . Is there any option to exclude power net but the effect will be captured in Signal net S parameter? 

Thanks for asking questions. In this case you can exclude Power net VDD by untick in the net manager. But if you want to get the effect of the power net shape , there is an option to turn it on.

To resolve this, enable the shapes of the power net (for example, VDD) even when the net itself is disabled. You should also select the Keep shape enabled when the net is disabled check box in the Net Manager section in PowerSI tool.

Enabling the shape ensures that the electromagnetic coupling effects are still captured, thus leading to more consistent S-Parameter results regardless of the power net's enabled state.