Just found this at usingmac‘s Tweek Screencapture Behavior post. There a few more tweaks in their article but this is the one that works for me personally.
When we used key combination [Cmd-Shift-4] + [Space], we will be able to capture a snapshot of window along with the shadow. The following command lines are used to disable the shadow.
defaults write com.apple.screencapture disable-shadow -bool true
killall SystemUIServer
You can change -bool true to -bool false to enable back the shadow.

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