If mass and matter cannot be created nor destroyed, then how does Mystique get taller or shorter, for example when she
imitates Trask in X-Men: Days of Future Past
Do her atoms and organs simply rearrange themselves? Does she become more dense?
In the X-Men Cinematic Timeline, we have been given no canon to explain her morphogenic abilities. Given that the Hulk acquires 600+ pounds during his transformation, there is no reason Mystique couldn't do the same.
In the canon Earth-616 Timeline
In the previous Scifi-Stack Exchange Question: Can Mystique CREATE Objects? The canon character received an update to her powers and abilities in the classic Marvel style.
Mystique's powers increased dramatically from shape-shifting to shape-changing.
In the X-Men movies universe
According to the Official Handbook of the Marvel Universe: (corrections)
The fully canon explanation would be that if she appears to be more massy (as she grows in stature), it's likely to be a matter of appearance. She may be holding onto the ground or stamping to give the impression of greater weight.
Similarly, her organs have proven to be very flexible. In the latest reboot (post X-Men forever) she is able to flatten herself, Mr Fantastic-style as well as generating machine objects and animal forms. This means that it's quite likely that as she grows or shrinks, she simply rearranges her organs to suit her outward form and she may be able to alter her molecular structure.