I'll point out one thing about key cloning, if you ever need to reset the module and register the keys; you won't be able to because you only have 1 key code. Which means it will have to go to the dealer to be reseeded, which will be expensive and cannot be done by anyone but a dealership or Toyota certified/approved locksmith/shop. You can add/register new keys as long as you have 1 Master Key, if you don't you're SOL.
As for the keys, well they are all-in-one units; that's how most keys are these days (they used to be separate chipped keys and fobs.) The "Smart" Keys are a little more expensive (about $300 for just the key.) It depends on the cut of the key itself, I don't remember if they are now using a new key pattern vs. the older keys that 4th gens used, not to mention if the security code is compatible (meaning that you may not be able to get a 4th gen key and have it cut and programmed the same.)
There are companies that sell "blank keys" on Ebay and Amazon, from what I have heard you get what you pay for. Usually most of them are willing to exchange DOA keys, but some can be a pain about it (I remember one member said they had to get like 3-4 keys before one finally worked and they were in the process of fighting for their money back.)
Either way, welcome to owning a modern vehicle; nothing is cheap anymore.
As for people losing stuff? You'd be surprised what goes missing/breaks with some people. I had a lady who came in once with 400miles on the odo with a small fender bender in the rear, then next week she comes in with the whole front end crunched up. Some people should just not be allowed behind the wheel.