By RAW, they get cover -- doesn't matter. Invisible creatures don't affect your aim per se, but they are meaty shields all the same. If I make a wall out of meat and hide behind it, even though it may be invisible, you still have to pass through it to get to me.
Still, you'd probably be aware of any shot that suddenly went askew because something was standing in its way, and thus aware of the creature there. Invisible isn't hidden -- most of the time, you're aware of where an invisible creature is, and aware that there's a creature there, too.