Johnny is not gonna think "Huh. Hundreds, if not, thousands of crows are all coming at me at once. I should probably use the two abilities that don't help whatsoever instead of using the one thing I know for a fact will save from any attack coming my way."
Also, Johnny's body control is nowhere near potent enough to survive it. Elasticity helps, but it only when he's getting crushed, squashed, squeezed, etc. It doesn't help when you're pecked by hundreds to thousands of crows.
Besides, Johnny is heavily reliant on his equipment in his base, so that makes him using an actual useful ability all the more likely.
Also, "a sea of black" really depends on how far the crows are from Johnny.