I personally like the shard design, but so far I love all of your concepts, so I trust that you'll end with something great.
I am against merging the HP bar with the reproduction bar. They show very different things and it will be very unintuitive to the player. Plus, health and reproduction, albeit related, are still very different things, so we definitely do not need to merge the two.
Final point, it might make sense to separate out the ATP compound from the bottom of the screen with glucose, oxygen, etc. and put it below the health bar. With the new compound system, the level of ATP should stay relatively constant as long as the cell is getting all the necessary nutrients. Separating it out will, first of all, draw attention to it (and ATP is fairly important to be noticeably different from all the other compounds) and will also show the player why he cannot move/health is going down/proteins aren't being synthesized.