I think we could indicate a bonus state being applied by having a slightly-transparent green effect/overlay being applied to a placed hex, similar to Civilization VI when placing hexes:
So that would effectively mean that the the entire surface area of a cell would have a slight green tint. Perhaps the exact bonus value could be represented in a similar manner as well by hovering over the part. And if the player wishes, they might be able to toggle off this perspective.
I think internal organelles as a whole get bonuses, though the extent to which this bonus occurs can vary a bit. I would think that for photosynthetic parts, the bonuses would be the strongest, incentivizing phototrophic organisms to maximize surface area similar to a leaf/rod. We can dive into more detailed explanations of bonuses if we agree on the visualization.
Regarding the tutorial: having a visual indicator like the green overlay can ease explanations for the mechanic. If we mention that organelles receive a slight bonus from being placed adjacent to the surface, and reinforce this with the green display, that might be sufficient.
The flagella/pili/cilia dilemma is a good point. Would the game be able to figure out if a certain organelle is covered by the flagella, hence taking away the bonus? Or would that only be based on the exact placements in the editor?