It really won't be difficult to surprise Shinji - and that's taking into account the fact that he saw Ken and Kotone messing around in the kitchen. Ken had help who knows what she's doing, so he left them alone.

(If it'd been Fuuka, he probably would've felt required to step in, even knowing Kotone got her to 'more or less edible cooking' while he was out of commission.)

In any case, he just got back from work and is still in the living room, if Ken does want to surprise him.