That's correct. The phone has an application that scans for modified system files and will detect that you're rooted. Then, when you boot, it'll show an image of an open padlock and the word "Custom" for a few seconds before continuing the boot.
Some people freak out over that. However, you don't have much choice here. If you want it rooted, then you're changing files on the ROM. That's customizing it, and will be detected. If you don't want it to show up as "Custom", then you want a factory stock device.
No. First, it's fairly likely that taking the Kit Kat 4.4 update will fail if you've modified your phone. You'll need to return it to very close to stock for 4.4 to apply cleanly.
Second, if you go to Kit Kat, your phone will be unrooted, Safestrap recovery will be removed, and you'll be stuck with a kernel that currently is not rootable. If you have a Verizon or AT&T phone (or any other with a locked bootloader), you won't be able to root it at the moment, so won't be able to do anything else.
Once VZ releases 4.4, we'll work on ways to get past factory stock, but that's not guaranteed to be successful until we see what VZ gives us.
Edit: And no, once you've updated to Kit Kat, you can't downgrade to 4.3. You'll need to use ROMs compatible with the 4.4 kernel.
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