Just moved from Houston, had a '12 jku Sahara with a hardtop. I personally sold the hardtop after about a month and got a trektop nx. I had a condo with a tiny garage so storage was not possible. I lived in the Heights area, but it was still houston so you do have to worry about getting your car broken into. No one messed with jt luckily. I just never kept anything valuable in it, and if someone really wanted in, they could break any window in the hardtop anyways.
I think the trektop soft top was way easier to quickly fold back than to remove the freedom panels, place them into their canvas bag, and then store them. In the month I had the hardtop I took the freedom panels off twice.
After I got the soft top, I rode in sun rider position on 50% of the non rainy days, and periodically took the back windows off etc.
It does rain in Houston, quite a bit. I never had a problem with the soft top leaking from natural rain, but I did get some leakage when going through an automatic car wash from the sideways shooting jets. I fixed that with some foam insulation tape along the frame up front.
Oh, even if you stick with the hardtop and go with the freedom panels off or use a soft top, I recommend spyder web shade to keep the Houston sun from beating you down. It's just enough shade to cool you down and not get burned, but still feels very open. And also keeps bird poop off you too.