In my past experience Apple Stores don't know you have JB your phone, assuming you restored it prior to return. And just hacking, not unlocking, hasn't bricked any phones in the past.
You will only lose your hacks if you run an Apple update. Don't update and you won't lose anything. Remember, you don't have to run any Apple updates. If you run an update you will have to wait until the new JB method has been discovered; and that's anyone's guess.
If you are nervous about doing it, don't. If you are unfamilair with SSH, Terminal, sFTP, CHMOD, permissions, etc. wait until you have done more reading as you will need those skills. On the plus side, I learned a lot about UNIX and using Terminal specifically from hacking my iP.
The biggest CON I have noticed is the realization that stock iPhones are kind of lame. 😀