Is it safe to cover babies hands with in built mittens from onesies over night? I have read that it stops them from flailing arms around and scratching face at night. But is it safe to sleep with hands covered?

I am unaware of any specific reason that wearing mittens would reduce the effect of startle reflex - swaddling/wrapping baby does in most babies.
How old is your baby?

Some babies like to suck their fingers, so mittens would make that difficult.

Let me know the age of you baby, as this may influence further response.