An elevated application does see the mapped drives for the user. This is similar to a service logging in under a user account and the user logging into the desktop with the same user account. The service won't be able to see the user's mapped drives.
A work around for this type of situation is to create a service that runs with the permissions you require and then a standard application that runs non-elevated. The application sends messages to the service so that it can perform the actions that need elevation.