The new aero model in KSP 1.0 changed the way cargo bays and fairings behaved in Kerbin's atmosphere, and so the Service Module fairing side panels need to be updated accordingly.

@Starwaster will look into this once he's finished with the DRE update for 1.0 and had some time to relax :)

Commits b08896b and fbae2bf now add stock drag occlusion for the pod cover and SM side fairings, using an updated version of the AnimatedDecouplers dependency to provide new decoupler part modules compatible with the stock ModuleCargoBay.

Awaiting user testing and feedback.

User responses so far have been quite positive, but I'll need a bit more confirmation.

@Starwaster and I consider this one to be fixed, with the following edge-case exception:

With the exception that separated shielded items will stay shielded if they weren't properly decoupled or otherwise came apart accidentally. Stock issue but I'll put some extra handling in AnimatedDecouplers so that they will handle it, and hopefully the stock bug will get fixed soon.

According to @NathanKell, this isn't going to be possible for many add-ons using the old fairing system like SDHI:

• Multipart (i.e. not fully enclosed) fairings do not work right now. They would need a plugin to work.
• The only drag occlusion is stack occlusion. Take a boost protective cover as an example. If the boost cover is mounted directly atop the pod, it will occlude the pod's drag; if you mount a docking port first, then the cover, you'll get essentially doubled drag (near full cross-sectional area from the pod since only the top bit is occluded by the docking port, then the same for the cover.)

A custom plugin would add yet another dependency to SDHI, which would prompt additional negative reaction from the subset of the userbase whose maxim is "the fewer (or no dependencies), the better".

EDIT: Since many similar add-ons are affected in the same manner, I suppose the reaction wouldn't be so bad.