Yes, you can drill into a kayak and mount gear tracks and certain other parts. If you do drill, you will want to use waterproof silicone to keep the holes water tight. Also, if you do not have access to the inside for backing, then you can use pop rivets. 5/16″ or 1/4″ are common sizes for many of the off-the-shelf kayak fishing accessories. Keep in mind when drilling that if your modification later causes a failure point, that the warranty will not cover it. But adding small accessories and tracks are not usually linked back to any sort of hull failure as long as you go slow and be careful!
Be sure to share your modification questions with the Vibe Owners Group on Facebook! They love to offer advice and share ideas!