Can Bone Skewer choose a unit that says it "can't be chosen by enemy spells and abilities"?
Yes. The unit's untargetability ability is inactive while the card is in hand, and Bone Skewer's choice does not target it.
"I can't be chosen by enemy spells and abilities" is a passive untargetability ability.757757.1 Passive abilities of permanents are typically active only while they are on the board.365.1 An ability that functions in another zone describes that context itself,366.1 which this ability does not, so it has no effect in hand. Separately, a card in hand is not a target because the hand is not a public zone.355.10.a