Yes it will. They even demoed the OS on N9s, but the good question is, whether they'll actually release it for the N9.
In any case, the N9 will benefit a free operating system from Mer and Nemo UX - which will be application compatible with Sailfish.
And if the system itself is fairly modular AND the hardware is open then there should be no stopping you from replacing the closed bits. But that's a big if.
There's three parts to this puzzle here. Mer, which is the core distribution. Nemo UX, an open source UI for phones built on top of Mer. Lastly, there's the Sailfish UI, which is the proprietary, Nemo-compatible Jolla-look&feel UX.
It's currently possible to build Mer along with Nemo for N900/N950/N9 (along with several non-Nokia devices), but as far as I understand, the Nemo UI is not usable for the former device. The Mer wiki has quite a lot of relevant information on the topic.
It is much easier to suggest solutions when you know nothing about the problem.