If you do %HP damage to a shield champion, the shield blocks the damage but doesn't count towards your current HP when calculating how much damage the ability does.
Morgana has 500 HP total and is currently at 200 HP. Elise's Q is dealing 40 magic damage + 8% of current health. So it will deal 56 damage to Morgana (obviously reduced by MR). If Morgana barriers while at 200 HP, bringing her effective HP to 315, Elise's Q will still deal 56 damage to Morgana's shield.
The same effect happens when Morgana uses her own black shield (which is obvious when considering the result from barrier, but we tested it anyway).
As a side note, if you take damage from a skill that only deals damage to your Barrier, that damage isn't listed in your death recap. Also, Morgana's black shield results in strange rounding errors.
Keywords to help out people who are trying to google this question like I was last night: League of Legends, shields block percent HP damage, shields block percent health damage, shields block damage based on current health, damage based on current health and shields, current health damage and shields