Upgrading a hand type only affects the score when exactly that hand is played, not hands that contain others. For example, upgrading high card only affects the hand if there is no other hand available.
Conversely, jokers that specify 'hands containing x' can apply to wider hands, e.g. hands containing 3 of a kind' is 3 of a kind, 4 of a kind, full house etc.
IIRC the only exception to this is that 4 of a kind doesn't contain 2 pair.