Yup, I capture them all the time. How often you come across them after finishing the main story depends on your progress when you completed The Last Watch. When I finished, I had only destroyed the first major hub array, Alpha. That left the other four major hub arrays intact and all their minor arrays. If you go after the minor arrays one at a time and leave the corresponding major hub last, you'll be spawning a lot of Watchtower ships as you destroy each minor array. Now if you've destroyed all five major hubs, then the chance meetings with Watchtower ships goes way down. There is a gameplay setting where you can increase or decrease the chance of Watchtower ambushes. I have it set to give the most chance and I still rarely see random ambushes. You can capture them on the ground, but they're not supposed be captured planet side. As you've probably observed, they tend to land quite a distance away and then immediately take off. I use this mod
https://www.nexusmods.com/starfield/mods/2952 to greatly slow time and increase the speed of my in game movements.