The only reason all derailleur bikes now have open runs of cable and more stops is because of the finicky nature of indexed shifting, prior to that, many would have enclosed cables. With a Rohloff, it'll make no difference, do whichever suits you and the bike.
What cables are you using?  Rohloff cables, and most of the alternatives, have sealed ends and there's no need to cut them before threading through the outer. If you're using something without, why? But if you already have them, then as Dan suggests, seal the ends. Also, the length isn't mm critical, you have the adjustment on the external box or the last stop on an internal shift. If you cut the outer a bit long, maybe an extra 2cm, you give yourself some extra leeway with the inner (Shortening the outer effectively lengthens the inner. Cutting the inner the right length shouldn't be an issue, it's only the exposed difference from the outer that matters.  For cutting the outer, I just measure it against the old one. The only awkward bit of changing cables is getting them wound the right way on the pulley, but even that just takes a bit of practice. 

I think your root problem is the cable fraying during installation. I have two suggestions that have worked well for me...

1) Cut your cables using clean, sharp cable cutters with V-shaped jaws.

2) Apply a drop of super glue (preferably beta-cyanoacrylate, the kind that shows bonding rubber or leather on the package...it handles surface contamination better than the standard kind in my experience) to the end and allow to dry completely.

These two steps almost completely eliminate the possibility of the cable end fraying and make the task so much simpler and faster.

As to your quesiton about one continuous run of housing vs open runs and cable stops...

One run of housing should make insertion for the cable easier to insert and it will eliminate some of the places where dirt and moisture can enter the housing segments.

I'd still want to use the v-cutters and super glue, though. It will pay off when it comes to secure the cable end.

Best, Dan.

...
To clarify, a “crack” sound could originate from many parts of the drive train (pedals, BB, etc). The sound I am attempting to describe only occurs once after shifting to any of the 8 to 14 gears and applying significant force to the pedals. After the crack sounds, continued pedaling or coasting and then putting much force into the pedals never causes the sound to occur again…..until shifting to a new 8-14 gear.
...

I have run out of ideas that would be unique to a Rohloff.

A strange thunking or clicking noise in a drive train can be hard to find.  Noises I have had that I was sure was in a bottom bracket or pedal area, or that I have heard others describe include:

• A clicking noise in a pedal, this was unusual because it was where I thought the noise was from. Sometimes, once per revolution.  Added grease to the pedal.   Fixed.
• Clicking noise in a bottom bracket.  Once per revolution.  I finally bought a new bottom bracket.  When I pulled my crank arms off the old one and then started to unthread the non-driveside bushing, it felt much looser than it should have been.  Instead of swapping bottom brackets, I tightened it.  That fixed it.
• Clicking noise when pedaling hard, twice per revolution.  A rear rack bolt that was tight, but not tight enough.  When I pedaled hard, there was enough frame flex that the stiff rack moved a bit under the bolt.  I diagnosed this by standing next to the bike, one hand on bike saddle, other hand on the rear brake lever holding brake hard, and one foot pressing on a pedal, then I could hear exactly where the click was.
• I have heard of others that solved a clicking noise by greasing a seatpost, the seatpost as they pedaled moved enough inside the seat tube to click.
• Loose square taper crank arm.
• Loose headset, but that noise should be from a location that you can't confuse with a rear hub noise.

I am sure that I could think of other issues, but none come to mind right now.

I assume this is chain drive, not on a frame capable of belt drive.  But if it is on a frame capable of belt drive, I would make sure the frame fittings for changing a belt are tight.

Being on a tandem, you have two bottom brackets, two cranks, that is more opportunity for places to make strange noises.

I know my list above is not specific to shifting, but it is all I could think of.

After posting this, came up with one more idea:  Loosen your shift cables slightly, maybe two or three turns on the cable adjusters.  Point being that if your cables are too tight, when you shift, the shift mechanism might not fully seat in the correct place inside the hub.

There is the Sunshine coast trail that you could start in Vancouver and it returns back to Vancouver and you can go via Victoria also take a look at the Kettle Valley trail in British Columbia as well. Without a vehicle at either end of trips here in Canada is a pain as we don't not have a decent public transport system like Europe.
I am from Yorkshire but have lived in BC for 47 years and come back to the UK for bike touring and have rail pass to duck out on the hard or wet day. I am off back to Scotland again this summer via visiting family in Yorkshire with a month long rail pass.

This is an immaculate model I purchased back in 2019 with the intention of cycling to Australia. Sadly, it managed only Lands End and Edgbaston for the cricket! It's been in dry storage ever since. The frame Geometry apparently suits someone in the 5'10'' to 6'5'' range.
It has very smooth 14 Speed Rohloff Hub gears, dynamo lights & a Brooks leather saddle. The front and back racks allow an ample load & there are lots of extras like crucial spare parts and front suspension forks if you wanted more 'off road'. SPD shoes thrown in if you're size 45. I'll possibly sell the Ortlieb panniers too. Photos should be attached hopefully.
I'm located just north of Bath in Malmesbury ( SN16 postcode ). 07500 657918. Offers close to £2000 considered.