The reason shelties vary so much in size is because it wasn't that long ago that collie was crossed in. Best guess is the sheltie came from Less than 100 years ago, as late as the 1930's that it's on record. There were also smaller collies being registered as shelties... that sort of thing. I would guess into the 1950's at least collie shenanigans were going on, if not longer, but it's hard to know for sure since stuff became very political and was not openly documented. Obviously you aren't likely to find (reliable) record of "so-and-so was a collie registered as a sheltie!" And then there's the matter of dogs who weren't registered at all.
To complicate matters, earlier in the breed's history there were smaller breeds. Possibly pomeranian, papillon, samoyed - nobody is quite sure.
So size is still being ironed out as a result of the breed's relative youth. There's also the matter of increasing popularity of the breed and BYBs/mills getting their hands on it. Happy was HUGE. If you're a BYB you really don't care about size. BUT even the best of breeders can have dogs go out of size. Payton is currently just out (over 16") unless his shoulders drop in maturity which happens. Typically you don't see itty bitty shelties or monster shelties like Hap if people know what they're doing, but it does happen. It's more common to see dogs who are just slightly under or slightly over.
Also, you can have puppies in a single litter vary widely in size. You're on my Facebook so you can see this picture... in Auggie's album, the family portrait (with a green background), all four dogs on the top row are from the same litter. The one on the far left is a BIG boy and the one second from the right is a tiny little guy, haha. Size genetics is frustrating stuff for sheltie breeders right now.
12" would be TINY. Even Princess Georgie the Tiny is between 13 1/4 and 13.5... not gotten a solid measure on her yet because really all we cared about was "over 13." But it could happen. I bet he's bigger than that though.
There are size charts for puppy growth. There is one in Sheltie Talk and there's a second one online that was compiled with different data and is different, I would have to look for it, but it's still just a guess. You can try to predict. Payton's breeder thought he was going to go out based on the size chart and wanted to cut him. I was willing to take the risk, for a good long while in the middle there he was actually on track to stay in... then he had another growth spurt and there you go. Breeders also generally know how their dogs grow, when their growth spurts are and when they mature/finish growing. So they can make an educated guess. But ultimately it's all an educated guess. You will find breeders who held a dog back and it ended up going out of size... you will find people who altered a dog because it was out after a year, then once it hit 2-3 years old and maturity finished, the chest broadened and the shoulders dropped and the dog went back in size...
So I suppose the answer to how easy is it to guess how big a sheltie puppy will grow is... not as easy as you might think? LOL. If size is a big factor I would recommend going with an older rescue, older than 10 months and you should see the permanent height.
As far as ears go, some dogs have ears that tip genetically. I tried to set Auggie's and once it became obvious he wasn't show quality I just ended up giving up. He HATED having his ears set so it wasn't worth doing. They broke low rather than staying prick... those are Auggie's ears. I kinda wish I had kept trying to set them in hindsight. =P
But mostly they are set that way. Most breeders set all puppy ears as a rule because you can't really just 'wait and see' how ears turn out and then try to fix it later, so you just start that way.
Happy and Kota both had prick ears. Happy's were HUGE to match the rest of his monster body hahaha. Kota had small ears and I took my fingers and tuliped them over once and he looked silly, so it's a good thing they ended up prick on him I think, LOL. Auggie looks silly when his ears are up though, sometimes when he's REALLY excited, he'll tip his head back so his ears go up and then his ears STAY up for a while and OMG! He looks ridiculous.