from my experience, no. i had my tube rhino lined, and it does get hot on the floorboards near the firewall, but nothing too extreme. i've drove barefoot in the summer, and it was nothing uncomfortable.
but i have a yj, although i don't think the tj's are any different with regards to that
Depending on where you will with how much water or mud wheeling you do you might has well rip the carpet out and do the interior. Did that to mine as well and it looks good and now never have to worry if water gets inside
i Herculined my TJ. Came out pretty nice. I haven't really noticed the heat. I put in some rubber floor mats so maybe that is why. It hasn't faded and I reapplied once but it was just because I had a little left over in the can and there were a few touch up spots. Besides, you can always keep your carpet and throw it back in!
I don't know how true it is, but if you're thinking of Herculining, I'd order or buy soon. I heard a rumor that the price is going up in the middle of this month. I ordered mine off products54.com . The guy had good prices. Just lettin ya know