1) Correct. It doesn't really sound fair because the new company...

1) Correct. It doesn't really sound fair because the new company doesn't know they are infringing but if the new company was infringing on Yowie's patent claims, they could be asked for the profits made and told to stop making/selling. Yowie could also try and licence their patent to the infringing company and make easy coin.
2) Not quite. It all comes down to the earliest priority date which Yowie would have. The patent examiner who looks at the new company's patent has access to all patent applications, including those not available to the public yet (this is why patent examiners have fed govt security clearances). Assumedly they would see Yowie's and tell the new company they can't have their patent because of it.