Absorption HOMO-LUMO, canonical?
Short answer is yes, HOMO and LUMO refer to canonical orbitals, since only those have at least some physical meaning.

Two more remarks about that:

Koopmans' Theorem does only work if you add or remove one electron. 

If you change two or more electrons of your system (e.g. exciting one electron is first removing one, then adding one in another orbital) you get additional terms in energy difference between both states. Those terms are coming from the electron-electron interaction of the two changed orbitals/electrons.

In case of changing only one orbital, those additional terms do not appear since there is no electron-electron self-interaction.

Furthermore, the approximation of Koopmans' Theorem, that orbitals do not change (do not relax, remain stationary) on removing/adding electrons, gets worse the more electrons change.

Orbitals itself are only an approximation. Factorizing the total electronic wave function into orbitals is mathematically only possible for non-interaction electrons, or like in Hartree-Fock if you assume some mean-field for the electron-electron interaction. 
The resulting canonical orbitals do not always match the simplified picture based on our chemical intuition.