The Hohenberg-Kohn theorem, the foundation of DFT, is based on the energy functional of electron density $n(\mathbf{r})$ for a system of Coulomb-interacting electrons, placed in in the external electrostatic potential $V(\mathbf{r})$: $$ E[n]=-e\int d\mathbf{r}\:V(\mathbf{r})n(\mathbf{r})+\frac{e^2}2\int d\mathbf{r}d\mathbf{r}'\:\frac{n(\mathbf{r})n(\mathbf{r}')}{|\mathbf{r}-\mathbf{r}'|}+F[n] $$ The theorem states that:
1) the part $F[n]$ of the functional is universal [i.e. independent on $V(\mathbf{r})$];
2) the minimum of $E[n]$ is achieved on exact electron density $n(\mathbf{r})$ in the ground state of the system.
The proof of the theorem is based on existence of one-to-one mapping from the density $n(\mathbf{r})$ on the external potential $V(\mathbf{r})$ and then (via solution of the Schrodinger equation) on the ground state $N$-electron wave function $\Psi(\mathbf{r}_1\ldots\mathbf{r}_N)$.
However, it is clear that this mapping $n(\mathbf{r})\Rightarrow V(\mathbf{r})\Rightarrow\Psi(\mathbf{r}_1\ldots\mathbf{r}_N)$ is different for different numbers of electrons $N$, and thus we must use different universal functionals $F_N[n]$ for each $N$.
For example, two electrons ($N=2$), placed in the potential $V(\mathbf{r})$, will have the ground state wave function $\Psi(\mathbf{r}_1,\mathbf{r}_2)$, found from the Schrodinger equation: $$ \left\{-\frac{\hbar^2\nabla_1^2}{2m}-\frac{\hbar^2\nabla_2^2}{2m}-eV(\mathbf{r}_1)-eV(\mathbf{r}_2)+\frac{e^2}{|\mathbf{r}_1-\mathbf{r}_2|}\right\}\Psi(\mathbf{r}_1,\mathbf{r}_2)=E\Psi(\mathbf{r}_1,\mathbf{r}_2), $$ and their ground state electron density will be: $$ n_{N=2}(\mathbf{r})=2\int d\mathbf{r}_2\:|\Psi(\mathbf{r},\mathbf{r}_2)|^2 $$ (antisymmetry of the wave function is implied).
In the case of three electrons ($N=3$) in the same potential $V(\mathbf{r})$ we should solve \begin{eqnarray} \left\{-\frac{\hbar^2\nabla_1^2}{2m}-\frac{\hbar^2\nabla_2^2}{2m}-\frac{\hbar^2\nabla_3^2}{2m}-eV(\mathbf{r}_1)-eV(\mathbf{r}_2)-eV(\mathbf{r}_3)\right.\nonumber\\ \left.+\frac{e^2}{|\mathbf{r}_1-\mathbf{r}_2|}+\frac{e^2}{|\mathbf{r}_2-\mathbf{r}_3|}+\frac{e^2}{|\mathbf{r}_3-\mathbf{r}_1|}\right\}\Psi(\mathbf{r}_1,\mathbf{r}_2,\mathbf{r}_3)=E\Psi(\mathbf{r}_1,\mathbf{r}_2,\mathbf{r}_3)\nonumber \end{eqnarray} and find the density $$ n_{N=3}(\mathbf{r})=3\int d\mathbf{r}_2d\mathbf{r}_3\:|\Psi(\mathbf{r},\mathbf{r}_2,\mathbf{r}_3)|^2. $$
It is clear that the mappings $V(\mathbf{r})\Rightarrow n_{N=2}(\mathbf{r})$ and $V(\mathbf{r})\Rightarrow n_{N=3}(\mathbf{r})$ should be different, i.e. the same $V(\mathrm{r})$ will generate different density profiles in two- and three-electron systems.
Now the question: why the dependence of the universal density functional $F_N[n]$ on the number of electrons $N$ is usually ignored?
Of course, in DFT calculations for many-electron systems (e.g., heavy atoms, complex molecules or solids) the difference between $F_N[n]$ and $F_{N+1}[n]$ can be negligible, thus we can use the limiting functional $F_\infty[n]$. However, the same functionals are often used and tested even for helium atom ($N=2$), for neon atom ($N=10$) and for solids ($N\rightarrow\infty$), and nobody bothers about different $N$ [see, for example F.G. Cruz et al., J. Phys. Chem. A 102, 4911 (1998)].