How are electronic configurations including hybrid orbitals notated? I know the general scheme for notating electronic configurations is (with s and p orbitals) [noble gas core]nsel.$n$pel. etc., where $n$ is the principal quantum number and el. is the number of electrons occupying that subshell, e.g. carbon: [He]2s22p2.

Now, how do you include hybrid orbitals? The problem arises because some hybrid orbitals already have superscript numbers (sp2, sp3 …) – how do you differentiate between these superscript numbers and those denoting how many electrons fill that orbital? If I were to write out the electronic configuration for the hybridised carbon atom in $\ce{CO2}$, this would not be a problem: [He]2sp22p2, but what about the carbon atom in $\ce{CH4}$, which has sp3 orbitals? Would you write [He]2sp3, 4 or [He]2sp34 or something else?
The electronic configuration concept does not really extend itself well to hybrid orbitals, because these are best considered mathematical concepts only. However, the problem is easily solveable:

Always use brackets when dealing with hybrid orbitals.

Even your $\ce{CO2}$ case is potentially misleading: I misread it once as $\mathrm{2s^1\ 2p^2}$. It is best to show what belongs together with: $\mathrm{[He]\ 2(sp)^2\ 2p^2}$ or, for methane: $\mathrm{[He]\ 2(sp^3)^4}$.