$3N$ is the number of available vibrational modes, where $N$ is the number of atoms in the solid. Each mode can have a non-negative number of phonons, so the total number of phonons is not $3N$. In thermal equilibrium, the average number of phonons in each mode is given by Bose-Einstein distribution with zero chemical potential.
Consider a 1D harmonic oscillator. The eigenstates of the oscillator are characterized by the "the number of phonons" $n$, and the energy eigenvalues are $\hbar \omega_0(\frac 1 2 + n)$ where $\omega_0$ is the classical frequency of the oscillator. To use the phonon terminology, there is only one vibrational mode occupied by $n$ phonons. $n$ can be any non-negative number.