You could do it without requiring $\emptyset \in \tau$. But if you do not want to exclude more or less all interesting spaces (like the reals with its standard topology), then the standard intersection axiom $(I)$ must be replaced by
$(I')$ $\phantom{x}$ If $A_1, \dots, A_n \in \tau$, then $\bigcap_{i=1}^n A_i \in \tau$ or $\bigcap_{i=1}^n A_i = \emptyset$.
Anyway, the system $\tau' = \tau \cup \{ \emptyset\}$ is again a topology in your modified sense, and it satisfies the intersection axiom in its original form. This is a much more elegant formulation which eliminates the special status of $\emptyset$ in the intersection axiom. Moreover, as the other answers have shown, the absence of $\emptyset$ as an open set would require to add another unnecessary special case to the definition of a continuous function.
Also note that if we work with $\emptyset \in \tau$, then the union axiom is satisfied also for the empty index set. This is just a very formal reason, but again it allows to avoid to consider an unnecessary special case.
Similarly you could omit the requirement $X \in \tau$. In that case you should replace the standard union axiom $(U)$ by the weaker version
$(U')$ $\phantom{x}$ If $(A_i)_{i \in I} \in \tau$, then $\bigcup_{i \in I} A_i \in \tau$ or $\bigcup_{i \in I} A_i = X$.
Once more there is no benefit in doing so. The system $\tau' = \tau \cup \{ X \}$ is again a topology in the modified sense, and it satisfies the union axiom in its original form without a special treatment of $X$. And the absence of $X$ as an open set would require to add another unnecessary special case to the definition of a continuous function. In fact, $f^{-1}(V) = X$ is possible for a continuous function $f : X \to Y$ and open $V \subsetneqq Y$. Finally, if we work with $X \in \tau$, then the intersection axiom is satisfied also for the empty index set.
Let us call a system $\tau \subset \mathcal P (X)$ a quasi-topology if it satisfies $(I')$ and $(U')$. We do require neither $\emptyset \in \tau$ nor $X\in \tau$. The following facts show that it does not make much difference to work with topologies or with quasi-topologies.
Each topology is a quasi-topology.
For each topology $\tau$, the "reduced set" $r(\tau) = \tau \setminus \{ \emptyset, X\}$ is a quasi-topology contained in $\tau$. Other quasi-topologies contained in $\tau$ are $r_U(\tau) = \tau \setminus \{ \emptyset\}$ (which satisfies $(U)$) and $r_I(\tau) = \tau \setminus \{ X \}$ (which satisfies $(I)$).
For each quasi-topology $\tau'$, the "extended set" $e(\tau') = \tau' \cup \{ \emptyset, X\}$ is a topology.
One has $e(r(\tau)) = \tau$ and $r(e(\tau')) \subset \tau'$. It is possible that $r(e(\tau')) \ne \tau'$.