Dear Sathiya Sir,
When the kitchen is in NW, the position itself is not that good but still, facing North while coocking is better than facing West.
Now, about toilet in SE: Yes S-E means Agneya direction is for Agni Tatva and in your case there is Bathroom-Toilet in that place. Agni & Jal are opposite tatva causing health issues. That is why your wife may be facing some heath issues. Please correct me, whether it is exactly in corner or differing corner towards south or towards west. As a measure, you can put a Red colour bulb in the toilet & apply red colour to the door from inside. This will minimize the vastu dosha.