Are turing machine really countable?
You are technically right. The correct phrasing should be that there are countably many TMs up to isomorphism of the tape alphabet and the state-space. 

Indeed, if you say that a TM with states $\{q,r\}$ is different than the same TM with states named $\{1,2\}$, then not only are TMs not a countable collection, they are not even a set in the ZFC axiom system.
This follows from the fact that the collection of all sets is not a set itself.