Will be an own opinion from myself.
As it is an upgrade, and the system also uses some of the old folder/file directories too, they MAY be kept in place.
It all comes down eventually if one is committed to update the things present and slowly move towards a independent v2 system (so gradually). When updating/upgrading the older system the links to wiil also still point to the old paths.. so if you change one, you will have to change the companionship too.
This will be the case for downloads etc.. also, the original files are stored in e107_files/downloads.. and in v2 there is no such folder, but new ones will go into media/..../