Chancey shots through limbs is never good!
Without seeing what your talking about, you need to ask yourself...
If you can't make an ethical shot through the limb openings, then you need to open your shooting lane.
Just remember they are arrows and not bullets, along with, the wee hours of light never seem to show the limbs / branches / twigs.
To answer your last question about scaring the deer away, who really knows?
Each deer is different, some may be curious, some possibly want to eat the leaves.
I know of a few loggers that carry a gun in their rig and have shot deer coming into the logging yards, go figure?
However, I would caution that any change will put the deer on alert, so be selective.