I do not see why not, but it shouldn't be in the way of where your Kayak would sit (obviously). You have a number of different ways of accomplishing this. How many lights were looking to install?
You could simply drill an appropriate sized hole through the tubing (this course is dependent on how thick the walls of the tubing are). If you some means of fabrication, you could weld some pre-drilled tabs onto it at your desired location and mount the lights that way. I tell ya this however, those lights are going to sit REAL high.
Have you just thought about getting a low profile LED light bar? They can be had pretty cheap these days on amazon or fleabay and would sit perfectly underneath the point where your Kayak would protrude from the front of your rack. Again, if you have the means to fabricate, you could incorporate the mounting for the light bar in between the tubing that runs up on either side of your windshield.
(my .02? I would start with some bumper mounted lights. Much easier for your position. two on the outer ends and grab a cheapo raised bar/brush guard and mount another two close by each other on that directly in the middle.
Stop whining about the 'ride' - If your YJ ain't wrangling your soul free, then might I suggest you buy a stationwagon... at least you can fit all your bull**** in the back.