If you explicitly provide the independent variable your first formulation works.
@named sys = ODESystem([Dₜ(Dₜ(x)) + ω₀^2*x ~ 0], t)
If you explicitly provide the independent variable your first formulation works.
@named sys = ODESystem([Dₜ(Dₜ(x)) + ω₀^2*x ~ 0], t)