1.Nope, you'll be fine
2. If your restore process is to remove these when you restore, then you'd zap these in both Dev and Test unless you are doing something special in Test? I would if I were you for the same reasons as you have now!
3. Once you have done your mods in DEV and run TTL, you'll then probably need to carry out some manual mods such as WebAccess links. Check through the list of things TTL syncs up from the manual and fix up any that remain to be done by hand.
Personally I've moved away from TTL unless it is for a very, very short length of time. It can be very hard to lock down PROD sufficiently even over a fairly short period of time for you to be really confident that when you press the button nothing will come back to life that you previously deleted.Did you modify any queries, delete the odd list item or category, alter a mail in a process and so on. Did you crate a category that you didn't also mirror back in DEV If you are not sure TTL may not be for you. If LD could provide a tool to 'lock' production, that would be excellent. Until then, I'd take a look at Design Transfer. It takes some time to get used to, but you really know what is moving across from one environment to the other.
Just some thoughts by the way, YMMV and other people may well disagree with me- and that is all good.