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My understanding is that the colour schemes for Marine specialities (apothecaries white, librarians blue, etc.) pre-dates the Horus Heresy. Are there any examples of CSMs using these colours for their own specialist troops (Plague Surgeons, sorcerors, etc.)? Or was the idea of visually marking out the specialists lost when most of them re-branded themselves with new colours?

 Horla wrote:
My understanding is that the colour schemes for Marine specialities (apothecaries white, librarians blue, etc.) pre-dates the Horus Heresy.

Not exactly - some Legions used some of the future markings, but not completely. For example - some Apothecaries only had a white shoulder pad or arm, matching the original RT artwork:


The colour schemes as they are now were established in the Codex Astartes.

The Traitor legions don't use the speciality designs because those ranks don't exist in their forces. Most of the specialist colours come from post-heresy culture and the Codex Astartes.
As for pre-heresy designs, Librarians simply wore the colours of their Legion and were only marked out with charms/runes/weapons. Blue is their post-heresy colour following the dictates of the Codex Astartes.
Chaplains descend from the Word Bearers. The WB Chaplains were created from the heralds seen in the Legion in their pre-Lorgar days and originally they wore black armour. Lorgar made this group into the Chaplains who then spread to most of the other Legions. The Chaplains wore the colours of their Legion also. The Blood Angels, Iron Hands and Space Wolves all already had their own style of Chaplain by this point. After the razing of Monarchia, the WB Chaplains painted their armour black and then fell to Chaos becoming Dark Apostles. AFAIK the reason Loyalist Chaplains wear black is in mourning of the Emperor and the skull helm is the Emperor's death mask.
Apothecaries are incredibly rare in the Traitor legions and Renegade chapters as they often do not have the facilities and equipment needed to train potential candidates. Often they will not be seen on the battlefield as their worth is deemed too great to be risked. Apothecaries such as Fabius Bile will loan their skills to warbands to secure material or protection.

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This is not limited to specialist positions, but the colors of the Pallid Hand Death Guard detachment very closely mimic those of the Pre-Heresy DG colors: