Yamcha and Krillen acknowledge the fact that Super Boo can sense Ki now, this implies that their Ki sensing is completely reliable -furthermore, the artwork shows sensing Boo just as he arrived to the lookout. There is no reason to disregard their Ki sensing abilities, it corrupts the plot.
When Piccolo says 'haven't you noticed', this occurrs DIRECTLY after Boo does his power-burst, so clearly, Piccolo expects that Krillen should have caught onto this. However, he didn't have a reason to worry so he didn't -how do I know this? Because he puts emphasis on what Goku predicted.
There doesn't seem to be anything to suggest Initial Evil Boo is much different from Innocent Boo.