fourfa

Neither. Clipping parts visually out of the way does not ever eliminate drag.  As for part 2 of your question, yes open nodes cause increased drag, but mis-matched nodes are just as bad or worse. For instance, if your plane is Mk1 part -> RTG -> Mk1 part, you’ll have huge drag at both the 1.25m-to-0.625m and 0.625m-to-1.25m nodes (the RTG is 0.625m or Mk0 as the game sees it - look at the diameter of the green node before attaching, these tell you what matches)
The correct answer is service bay, cargo bay, or fairing.  That is the only way to eliminate drag entirely for your various service parts. All my SSTOs have one, and I test carefully that the parts inside are actually shielded from drag (it’s quite easy to have a part that looks like it should be shielded actually be getting drag). Try alt-F12 -> Physics -> aero -> show aero data in right-click menu (something like that), then right-click the part in question.
Aero mods like FAR change everything but since you didn’t mention it and are asking here instead of the FAR thread I’m assuming you’re playing stock

In general, the gyro wheels present on many spacecraft are for navigation.  "All spacecraft" is going too far these days - gyro-based inertial platforms are big, heavy, expensive, hot, and prone to errors and failures, compared to modern purely-electronic MEMS-based accelerometers.  Heck, some microsats that don't have the weight or power budget for true standalone navigation just use GPS and magnetic field sensors to grab their position and orientation.
There are real-world reaction wheels, to be sure.  KSP's versions are massively simplified, and are too powerful, too lightweight, don't draw enough electrical power, don't require cooling, don't require desaturation, don't fail, and generally violate the laws of motion  
Players going for realism often do deactivate the reaction wheels built-in to the command pods, and use RCS for attitude control.  There are many mods that nerf KSP's reaction wheels to force the player to spend a lot of design work on balancing their RCS placement and fuel quantity, as we do in the real world.  I'm fond of this one:
Because it nerfs RW power when you want to rotate the ship, but it uses full RW power when you want to simply hold orientation.  This avoids a problem with KSP's stock SAS, where it's tuned to expect some reaction wheel torque.  Without that torque, SAS tends to oscillate back and forth using RCS and dump all your RCS propellant.  For full realism with no reaction wheel torque at all, I'd recommend going with mods for attitude control (MechJeb, AtmosphericAutopilot etc) and seldom using the stock SAS.

You might be interested in this thread, particularly towards the end:
In which people play with how to stay at the ultimate top speed of the RAPIER (~1751m/s) for circumnavigation racing.  Lots of thermal problems to navigate.  Loads of creative designs.

Just to make this more explicit - you're running version 1.0.4.  1.1 was a major update in April 2016, 1.2 was a major update in October 2016.  There have been a couple smaller bugfix/updates since - the current version is 1.2.2.  The Kerbnet feature was part of the 1.2 update and didn't exist before that.
Any version purchased from any of the legal vendors is entitled to free updates to the current 1.2.  If you got yours through some other method - well, everyone here would like to see Squad continue to provide updates to this game, and game developer salaries are paid by buying games.  So you know what you should do in that case.

Red drag arrows, or an actual number readout of drag?  The arrows don't always reflect whether the game thinks parts are properly shielded or not.
Hit Alt-F12.  Go to Physics -> Aero -> and check 'Display Aero Data in Action Menus'.  Now right click the parts in question, and see if they say 'Shielded = True' or 'False'

There are broad tendencies that are similar - for instance poles usually have more ore than equatorial.  But on Easy or Normal game settings, it hardly matters because there is generally ore more or less everywhere.  Start a new sandbox game on the default Hard settings (where almost all surface area will be 0%), cheat a scanner to Minmus orbit.  Then start another one and do the same - you'll see differences.

Make sure you check "enable advanced tweakables" in the settings for that savegame

Some vestigial long-dead feature.  I watched a Squadcast with HarvesteR and Das where Harv expressed surprise that the 'blink lights' was still there

Nope. It's a vestigial feature from long ago. There is zero difference in drag open or closed

Sad to report - I loaded the ship in a 100% stock save and drag was properly occluded in the bay.  Should have gone there right away before posting.  Now to begin the process of weeding out.
In further news, AeroGUI tells me these errant thrusters are responsible for roughly 2-3% of total ship drag.  That's worth tracking down to me.
EDIT - RCS Sounds is the guilty party.  Marking this answered and headed to the mod thread.

There's a mod called NavHud that would help a lot